MutationT@ster 2025

NEVER press reload or F5 - unless you want to start from the very beginning.
Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000313654
Querying Taster for transcript #2: ENST00000399516
Querying Taster for transcript #3: ENST00000269217
Querying Taster for transcript #4: ENST00000587184
MT speed 0.23 s - this script 2.715486 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000313654(MANE Select)	LAMA3	Benign	16\|84	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000399516	LAMA3	Benign	35\|65	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000269217(MANE Select)	LAMA3	Benign	36\|64	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected
ENST00000587184	LAMA3	Benign	37\|63	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Heterozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

18:23933924C>T_1_ENST00000313654

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 16|84 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr18:23933924C>T (GRCh38)

Gene symbol

LAMA3

Gene constraints

LOEUF: 0.73, LOF (oe): 0.66, misssense (oe): 0.88, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000313654.14

Genbank transcript ID

NM_198129 (exact from MANE)

UniProt / AlphaMissense peptide

LAMA3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.8851C>T
g.244472C>T

AA changes

AAE:	R2951C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs61752346
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	10	3959	3969

Protein conservation

Species	Match	AA	Alignment
Human		2951	G	S	T	R	F	N	K	T	K	T	F	R	I	N	Q	L	L	Q	D	T	P	V	A	S
mutated	not conserved	2951		S	T	R	F	N	K	T	K	T	F	C	I	N	Q	L	L	Q	D	T	P	V	A
Ptroglodytes	all identical	2951		S	T	R	F	N	K	T	K	T	F	R	I	N	Q	L	L	Q	D	T	P	V	A
Mmulatta	all identical	2951		S	T	R	F	N	K	A	K	T	F	R	I	N	Q	L	L	Q	D	T	P	V	A
Fcatus	not conserved	2948	G	S	T	R	F	D	K	A	H	T	F	S	I	N	Q	P	L	R	D	T	P	A	A
Mmusculus	not conserved	2947	S	P	K	G	F	N	K	A	R	S	F	N	V	N	Q	L	L	Q	D	A	P	Q	A
Ggallus	all identical	2792									F	T	F	R	-	R	Q	A	L	Q	N	T	A	I	P
Trubripes	no alignment	n/a
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	not conserved	3072	D	F	R	S	Y	S	L	T	L	N	E	D	D	M	N	L	I	N	S	M	N	K	V

Protein features

Start (aa)	End (aa)	Feature	Details
36	3333	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.026	0
	-0.284	0
(flanking)	-1.257	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

18

Strand

1

Original gDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGGTAAGTGTC

Altered gDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGGTAAGTGTC

Original cDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGCTGTTGCAG

Altered cDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGCTGTTGCAG

Wildtype AA sequence

MAAAARPRGR ALGPVLPPTP LLLLVLRVLP ACGATARDPG AAAGLSLHPT YFNLAEAARI
WATATCGERG PGEGRPQPEL YCKLVGGPTA PGSGHTIQGQ FCDYCNSEDP RKAHPVTNAI
DGSERWWQSP PLSSGTQYNR VNLTLDLGQL FHVAYILIKF ANSPRPDLWV LERSVDFGST
YSPWQYFAHS KVDCLKEFGR EANMAVTRDD DVLCVTEYSR IVPLENGEVV VSLINGRPGA
KNFTFSHTLR EFTKATNIRL RFLRTNTLLG HLISKAQRDP TVTRRYYYSI KDISIGGQCV
CNGHAEVCNI NNPEKLFRCE CQHHTCGETC DRCCTGYNQR RWRPAAWEQS HECEACNCHG
HASNCYYDPD VERQQASLNT QGIYAGGGVC INCQHNTAGV NCEQCAKGYY RPYGVPVDAP
DGCIPCSCDP EHADGCEQGS GRCHCKPNFH GDNCEKCAIG YYNFPFCLRI PIFPVSTPSS
EDPVAGDIKG CDCNLEGVLP EICDAHGRCL CRPGVEGPRC DTCRSGFYSF PICQACWCSA
LGSYQMPCSS VTGQCECRPG VTGQRCDRCL SGAYDFPHCQ GSSSACDPAG TINSNLGYCQ
CKLHVEGPTC SRCKLLYWNL DKENPSGCSE CKCHKAGTVS GTGECRQGDG DCHCKSHVGG
DSCDTCEDGY FALEKSNYFG CQGCQCDIGG ALSSMCSGPS GVCQCREHVV GKVCQRPENN
YYFPDLHHMK YEIEDGSTPN GRDLRFGFDP LAFPEFSWRG YAQMTSVQND VRITLNVGKS
SGSLFRVILR YVNPGTEAVS GHITIYPSWG AAQSKEIIFL PSKEPAFVTV PGNGFADPFS
ITPGIWVACI KAEGVLLDYL VLLPRDYYEA SVLQLPVTEP CAYAGPPQEN CLLYQHLPVT
RFPCTLACEA RHFLLDGEPR PVAVRQPTPA HPVMVDLSGR EVELHLRLRI PQVGHYVVVV
EYSTEAAQLF VVDVNVKSSG SVLAGQVNIY SCNYSVLCRS AVIDHMSRIA MYELLADADI
QLKGHMARFL LHQVCIIPIE EFSAEYVRPQ VHCIASYGRF VNQSATCVSL AHETPPTALI
LDVLSGRPFP HLPQQSSPSV DVLPGVTLKA PQNQVTLRGR VPHLGRYVFV IHFYQAAHPT
FPAQVSVDGG WPRAGSFHAS FCPHVLGCRD QVIAEGQIEF DISEPEVAAT VKVPEGKSLV
LVRVLVVPAE NYDYQILHKK SMDKSLEFIT NCGKNSFYLD PQTASRFCKN SARSLVAFYH
KGALPCECHP TGATGPHCSP EGGQCPCQPN VIGRQCTRCA TGHYGFPRCK PCSCGRRLCE
EMTGQCRCPP RTVRPQCEVC ETHSFSFHPM AGCEGCNCSR RGTIEAAMPE CDRDSGQCRC
KPRITGRQCD RCASGFYRFP ECVPCNCNRD GTEPGVCDPG TGACLCKENV EGTECNVCRE
GSFHLDPANL KGCTSCFCFG VNNQCHSSHK RRTKFVDMLG WHLETADRVD IPVSFNPGSN
SMVADLQELP ATIHSASWVA PTSYLGDKVS SYGGYLTYQA KSFGLPGDMV LLEKKPDVQL
TGQHMSIIYE ETNTPRPDRL HHGRVHVVEG NFRHASSRAP VSREELMTVL SRLADVRIQG
LYFTETQRLT LSEVGLEEAS DTGSGRIALA VEICACPPAY AGDSCQGCSP GYYRDHKGLY
TGRCVPCNCN GHSNQCQDGS GICVNCQHNT AGEHCERCQE GYYGNAVHGS CRACPCPHTN
SFATGCVVNG GDVRCSCKAG YTGTQCERCA PGYFGNPQKF GGSCQPCSCN SNGQLGSCHP
LTGDCINQEP KDSSPAEECD DCDSCVMTLL NDLATMGEQL RLVKSQLQGL SASAGLLEQM
RHMETQAKDL RNQLLNYRSA ISNHGSKIEG LERELTDLNQ EFETLQEKAQ VNSRKAQTLN
NNVNRATQSA KELDVKIKNV IRNVHILLKQ ISGTDGEGNN VPSGDFSREW AEAQRMMREL
RNRNFGKHLR EAEADKRESQ LLLNRIRTWQ KTHQGENNGL ANSIRDSLNE YEAKLSDLRA
RLQEAAAQAK QANGLNQENE RALGAIQRQV KEINSLQSDF TKYLTTADSS LLQTNIALQL
MEKSQKEYEK LAASLNEARQ ELSDKVRELS RSAGKTSLVE EAEKHARSLQ ELAKQLEEIK
RNASGDELVR CAVDAATAYE NILNAIKAAE DAANRAASAS ESALQTVIKE DLPRKAKTLS
SNSDKLLNEA KMTQKKLKQE VSPALNNLQQ TLNIVTVQKE VIDTNLTTLR DGLHGIQRGD
IDAMISSAKS MVRKANDITD EVLDGLNPIQ TDVERIKDTY GRTQNEDFKK ALTDADNSVN
KLTNKLPDLW RKIESINQQL LPLGNISDNM DRIRELIQQA RDAASKVAVP MRFNGKSGVE
VRLPNDLEDL KGYTSLSLFL QRPNSRENGG TENMFVMYLG NKDASRDYIG MAVVDGQLTC
VYNLGDREAE LQVDQILTKS ETKEAVMDRV KFQRIYQFAR LNYTKGATSS KPETPGVYDM
DGRNSNTLLN LDPENVVFYV GGYPPDFKLP SRLSFPPYKG CIELDDLNEN VLSLYNFKKT
FNLNTTEVEP CRRRKEESDK NYFEGTGYAR VPTQPHAPIP TFGQTIQTTV DRGLLFFAEN
GDRFISLNIE DGKLMVRYKL NSELPKERGV GDAINNGRDH SIQIKIGKLQ KRMWINVDVQ
NTIIDGEVFD FSTYYLGGIP IAIRERFNIS TPAFRGCMKN LKKTSGVVRL NDTVGVTKKC
SEDWKLVRSA SFSRGGQLSF TDLGLPPTDH LQASFGFQTF QPSGILLDHQ TWTRNLQVTL
EDGYIELSTS DSGGPIFKSP QTYMDGLLHY VSVISDNSGL RLLIDDQLLR NSKRLKHISS
SRQSLRLGGS NFEGCISNVF VQRLSLSPEV LDLTSNSLKR DVSLGGCSLN KPPFLMLLKG
STRFNKTKTF RINQLLQDTP VASPRSVKVW QDACSPLPKT QANHGALQFG DIPTSHLLFK
LPQELLKPRS QFAVDMQTTS SRGLVFHTGT KNSFMALYLS KGRLVFALGT DGKKLRIKSK
EKCNDGKWHT VVFGHDGEKG RLVVDGLRAR EGSLPGNSTI SIRAPVYLGS PPSGKPKSLP
TNSFVGCLKN FQLDSKPLYT PSSSFGVSSC LGGPLEKGIY FSEEGGHVVL AHSVLLGPEF
KLVFSIRPRS LTGILIHIGS QPGKHLCVYL EAGKVTASMD SGAGGTSTSV TPKQSLCDGQ
WHSVAVTIKQ HILHLELDTD SSYTAGQIPF PPASTQEPLH LGGAPANLTT LRIPVWKSFF
GCLRNIHVNH IPVPVTEALE VQGPVSLNGC PDQ*

Mutated AA sequence

MAAAARPRGR ALGPVLPPTP LLLLVLRVLP ACGATARDPG AAAGLSLHPT YFNLAEAARI
WATATCGERG PGEGRPQPEL YCKLVGGPTA PGSGHTIQGQ FCDYCNSEDP RKAHPVTNAI
DGSERWWQSP PLSSGTQYNR VNLTLDLGQL FHVAYILIKF ANSPRPDLWV LERSVDFGST
YSPWQYFAHS KVDCLKEFGR EANMAVTRDD DVLCVTEYSR IVPLENGEVV VSLINGRPGA
KNFTFSHTLR EFTKATNIRL RFLRTNTLLG HLISKAQRDP TVTRRYYYSI KDISIGGQCV
CNGHAEVCNI NNPEKLFRCE CQHHTCGETC DRCCTGYNQR RWRPAAWEQS HECEACNCHG
HASNCYYDPD VERQQASLNT QGIYAGGGVC INCQHNTAGV NCEQCAKGYY RPYGVPVDAP
DGCIPCSCDP EHADGCEQGS GRCHCKPNFH GDNCEKCAIG YYNFPFCLRI PIFPVSTPSS
EDPVAGDIKG CDCNLEGVLP EICDAHGRCL CRPGVEGPRC DTCRSGFYSF PICQACWCSA
LGSYQMPCSS VTGQCECRPG VTGQRCDRCL SGAYDFPHCQ GSSSACDPAG TINSNLGYCQ
CKLHVEGPTC SRCKLLYWNL DKENPSGCSE CKCHKAGTVS GTGECRQGDG DCHCKSHVGG
DSCDTCEDGY FALEKSNYFG CQGCQCDIGG ALSSMCSGPS GVCQCREHVV GKVCQRPENN
YYFPDLHHMK YEIEDGSTPN GRDLRFGFDP LAFPEFSWRG YAQMTSVQND VRITLNVGKS
SGSLFRVILR YVNPGTEAVS GHITIYPSWG AAQSKEIIFL PSKEPAFVTV PGNGFADPFS
ITPGIWVACI KAEGVLLDYL VLLPRDYYEA SVLQLPVTEP CAYAGPPQEN CLLYQHLPVT
RFPCTLACEA RHFLLDGEPR PVAVRQPTPA HPVMVDLSGR EVELHLRLRI PQVGHYVVVV
EYSTEAAQLF VVDVNVKSSG SVLAGQVNIY SCNYSVLCRS AVIDHMSRIA MYELLADADI
QLKGHMARFL LHQVCIIPIE EFSAEYVRPQ VHCIASYGRF VNQSATCVSL AHETPPTALI
LDVLSGRPFP HLPQQSSPSV DVLPGVTLKA PQNQVTLRGR VPHLGRYVFV IHFYQAAHPT
FPAQVSVDGG WPRAGSFHAS FCPHVLGCRD QVIAEGQIEF DISEPEVAAT VKVPEGKSLV
LVRVLVVPAE NYDYQILHKK SMDKSLEFIT NCGKNSFYLD PQTASRFCKN SARSLVAFYH
KGALPCECHP TGATGPHCSP EGGQCPCQPN VIGRQCTRCA TGHYGFPRCK PCSCGRRLCE
EMTGQCRCPP RTVRPQCEVC ETHSFSFHPM AGCEGCNCSR RGTIEAAMPE CDRDSGQCRC
KPRITGRQCD RCASGFYRFP ECVPCNCNRD GTEPGVCDPG TGACLCKENV EGTECNVCRE
GSFHLDPANL KGCTSCFCFG VNNQCHSSHK RRTKFVDMLG WHLETADRVD IPVSFNPGSN
SMVADLQELP ATIHSASWVA PTSYLGDKVS SYGGYLTYQA KSFGLPGDMV LLEKKPDVQL
TGQHMSIIYE ETNTPRPDRL HHGRVHVVEG NFRHASSRAP VSREELMTVL SRLADVRIQG
LYFTETQRLT LSEVGLEEAS DTGSGRIALA VEICACPPAY AGDSCQGCSP GYYRDHKGLY
TGRCVPCNCN GHSNQCQDGS GICVNCQHNT AGEHCERCQE GYYGNAVHGS CRACPCPHTN
SFATGCVVNG GDVRCSCKAG YTGTQCERCA PGYFGNPQKF GGSCQPCSCN SNGQLGSCHP
LTGDCINQEP KDSSPAEECD DCDSCVMTLL NDLATMGEQL RLVKSQLQGL SASAGLLEQM
RHMETQAKDL RNQLLNYRSA ISNHGSKIEG LERELTDLNQ EFETLQEKAQ VNSRKAQTLN
NNVNRATQSA KELDVKIKNV IRNVHILLKQ ISGTDGEGNN VPSGDFSREW AEAQRMMREL
RNRNFGKHLR EAEADKRESQ LLLNRIRTWQ KTHQGENNGL ANSIRDSLNE YEAKLSDLRA
RLQEAAAQAK QANGLNQENE RALGAIQRQV KEINSLQSDF TKYLTTADSS LLQTNIALQL
MEKSQKEYEK LAASLNEARQ ELSDKVRELS RSAGKTSLVE EAEKHARSLQ ELAKQLEEIK
RNASGDELVR CAVDAATAYE NILNAIKAAE DAANRAASAS ESALQTVIKE DLPRKAKTLS
SNSDKLLNEA KMTQKKLKQE VSPALNNLQQ TLNIVTVQKE VIDTNLTTLR DGLHGIQRGD
IDAMISSAKS MVRKANDITD EVLDGLNPIQ TDVERIKDTY GRTQNEDFKK ALTDADNSVN
KLTNKLPDLW RKIESINQQL LPLGNISDNM DRIRELIQQA RDAASKVAVP MRFNGKSGVE
VRLPNDLEDL KGYTSLSLFL QRPNSRENGG TENMFVMYLG NKDASRDYIG MAVVDGQLTC
VYNLGDREAE LQVDQILTKS ETKEAVMDRV KFQRIYQFAR LNYTKGATSS KPETPGVYDM
DGRNSNTLLN LDPENVVFYV GGYPPDFKLP SRLSFPPYKG CIELDDLNEN VLSLYNFKKT
FNLNTTEVEP CRRRKEESDK NYFEGTGYAR VPTQPHAPIP TFGQTIQTTV DRGLLFFAEN
GDRFISLNIE DGKLMVRYKL NSELPKERGV GDAINNGRDH SIQIKIGKLQ KRMWINVDVQ
NTIIDGEVFD FSTYYLGGIP IAIRERFNIS TPAFRGCMKN LKKTSGVVRL NDTVGVTKKC
SEDWKLVRSA SFSRGGQLSF TDLGLPPTDH LQASFGFQTF QPSGILLDHQ TWTRNLQVTL
EDGYIELSTS DSGGPIFKSP QTYMDGLLHY VSVISDNSGL RLLIDDQLLR NSKRLKHISS
SRQSLRLGGS NFEGCISNVF VQRLSLSPEV LDLTSNSLKR DVSLGGCSLN KPPFLMLLKG
STRFNKTKTF CINQLLQDTP VASPRSVKVW QDACSPLPKT QANHGALQFG DIPTSHLLFK
LPQELLKPRS QFAVDMQTTS SRGLVFHTGT KNSFMALYLS KGRLVFALGT DGKKLRIKSK
EKCNDGKWHT VVFGHDGEKG RLVVDGLRAR EGSLPGNSTI SIRAPVYLGS PPSGKPKSLP
TNSFVGCLKN FQLDSKPLYT PSSSFGVSSC LGGPLEKGIY FSEEGGHVVL AHSVLLGPEF
KLVFSIRPRS LTGILIHIGS QPGKHLCVYL EAGKVTASMD SGAGGTSTSV TPKQSLCDGQ
WHSVAVTIKQ HILHLELDTD SSYTAGQIPF PPASTQEPLH LGGAPANLTT LRIPVWKSFF
GCLRNIHVNH IPVPVTEALE VQGPVSLNGC PDQ*

Position of stopcodon in wt / mu CDS

10002 / 10002

Position (AA) of stopcodon in wt / mu AA sequence

3334 / 3334

Position of stopcodon in wt / mu cDNA

10233 / 10233

Position of start ATG in wt / mu cDNA

232 / 232

Last intron/exon boundary

10087

Theoretical NMD boundary in CDS

9805

Length of CDS

10002

Coding sequence (CDS) position

8851

cDNA position

9082

gDNA position

244472

Chromosomal position

23933924

Speed

0.07 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

18:23933924C>T_2_ENST00000399516

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 35|65 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr18:23933924C>T (GRCh38)

Gene symbol

LAMA3

Gene constraints

LOEUF: 0.71, LOF (oe): 0.64, misssense (oe): 0.88, synonymous (oe): 0.90 ? (gnomAD)

Ensembl transcript ID

ENST00000399516.7

Genbank transcript ID

NM_001127717 (by similarity)

UniProt / AlphaMissense peptide

LAMA3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.8683C>T
g.244472C>T

AA changes

AAE:	R2895C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs61752346
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	10	3959	3969

Protein conservation

Species	Match	AA	Alignment
Human		2895	G	S	T	R	F	N	K	T	K	T	F	R	I	N	Q	L	L	Q	D	T	P	V	A	S
mutated	not conserved	2895	G	S	T	R	F	N	K	T	K	T	F	C	I	N	Q	L	L	Q	D	T	P	V	A
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
36	3333	CHAIN		lost
2767	2927	DOMAIN	Laminin G-like	lost
2895	2895	DISULFID		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.026	0
	-0.284	0
(flanking)	-1.257	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

18

Strand

1

Original gDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGGTAAGTGTC

Altered gDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGGTAAGTGTC

Original cDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGCTGTTGCAG

Altered cDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGCTGTTGCAG

Wildtype AA sequence

MAAAARPRGR ALGPVLPPTP LLLLVLRVLP ACGATARDPG AAAGLSLHPT YFNLAEAARI
WATATCGERG PGEGRPQPEL YCKLVGGPTA PGSGHTIQGQ FCDYCNSEDP RKAHPVTNAI
DGSERWWQSP PLSSGTQYNR VNLTLDLGQL FHVAYILIKF ANSPRPDLWV LERSVDFGST
YSPWQYFAHS KVDCLKEFGR EANMAVTRDD DVLCVTEYSR IVPLENGEVV VSLINGRPGA
KNFTFSHTLR EFTKATNIRL RFLRTNTLLG HLISKAQRDP TVTRRYYYSI KDISIGGQCV
CNGHAEVCNI NNPEKLFRCE CQHHTCGETC DRCCTGYNQR RWRPAAWEQS HECEACNCHG
HASNCYYDPD VERQQASLNT QGIYAGGGVC INCQHNTAGV NCEQCAKGYY RPYGVPVDAP
DGCIPCSCDP EHADGCEQGS GRCHCKPNFH GDNCEKCAIG YYNFPFCLRI PIFPVSTPSS
EDPVAGDIKG CDCNLEGVLP EICDAHGRCL CRPGVEGPRC DTCRSGFYSF PICQACWCSA
LGSYQMPCSS VTGQCECRPG VTGQRCDRCL SGAYDFPHCQ GSSSACDPAG TINSNLGYCQ
CKLHVEGPTC SRCKLLYWNL DKENPSGCSE CKCHKAGTVS GTGECRQGDG DCHCKSHVGG
DSCDTCEDGY FALEKSNYFG CQGCQCDIGG ALSSMCSGPS GVCQCREHVV GKVCQRPENN
YYFPDLHHMK YEIEDGSTPN GRDLRFGFDP LAFPEFSWRG YAQMTSVQND VRITLNVGKS
SGSLFRVILR YVNPGTEAVS GHITIYPSWG AAQSKEIIFL PSKEPAFVTV PGNGFADPFS
ITPGIWVACI KAEGVLLDYL VLLPRDYYEA SVLQLPVTEP CAYAGPPQEN CLLYQHLPVT
RFPCTLACEA RHFLLDGEPR PVAVRQPTPA HPVMVDLSGR EVELHLRLRI PQVGHYVVVV
EYSTEAAQLF VVDVNVKSSG SVLAGQVNIY SCNYSVLCRS AVIDHMSRIA MYELLADADI
QLKGHMARFL LHQVCIIPIE EFSAEYVRPQ VHCIASYGRF VNQSATCVSL AHETPPTALI
LDVLSGRPFP HLPQQSSPSV DVLPGVTLKA PQNQVTLRGR VPHLGRYVFV IHFYQAAHPT
FPAQVSVDGG WPRAGSFHAS FCPHVLGCRD QVIAEGQIEF DISEPEVAAT VKVPEGKSLV
LVRVLVVPAE NYDYQILHKK SMDKSLEFIT NCGKNSFYLD PQTASRFCKN SARSLVAFYH
KGALPCECHP TGATGPHCSP EGGQCPCQPN VIGRQCTRCA TGHYGFPRCK PCSCGRRLCE
EMTGQCRCPP RTVRPQCEVC ETHSFSFHPM AGCEGCNCSR RGTIEAAMPE CDRDSGQCRC
KPRITGRQCD RCASGFYRFP ECVPCNCNRD GTEPGVCDPG TGACLCKENV EGTECNVCRE
GSFHLDPANL KGCTSCFCFG VNNQCHSSHK RRTKFVDMLG WHLETADRVD IPVSFNPGSN
SMVADLQELP ATIHSASWVA PTSYLGDKVS SYGGYLTYQA KSFGLPGDMV LLEKKPDVQL
TGQHMSIIYE ETNTPRPDRL HHGRVHVVEG NFRHASSRAP VSREELMTVL SRLADVRIQG
LYFTETQRLT LSEVGLEEAS DTGSGRIALA VEICACPPAY AGDSCQGCSP GYYRDHKGLY
TGRCVPCNCN GHSNQCQDGS GICVNCQHNT AGEHCERCQE GYYGNAVHGS CRACPCPHTN
SFATGCVVNG GDVRCSCKAG YTGTQCERCA PGYFGNPQKF GGSCQPCSCN SNGQLGSCHP
LTGDCINQEP KDSSPAEECD DCDSCVMTLL NDLATMGEQL RLVKSQLQGL SASAGLLEQM
RHMETQAKDL RNQLLNYRSA ISNHGSKIEG LERELTDLNQ EFETLQEKAQ VNSRKAQTLN
NNVNRATQSA KELDVKIKNV IRNVHMLNRI RTWQKTHQGE NNGLANSIRD SLNEYEAKLS
DLRARLQEAA AQAKQANGLN QENERALGAI QRQVKEINSL QSDFTKYLTT ADSSLLQTNI
ALQLMEKSQK EYEKLAASLN EARQELSDKV RELSRSAGKT SLVEEAEKHA RSLQELAKQL
EEIKRNASGD ELVRCAVDAA TAYENILNAI KAAEDAANRA ASASESALQT VIKEDLPRKA
KTLSSNSDKL LNEAKMTQKK LKQEVSPALN NLQQTLNIVT VQKEVIDTNL TTLRDGLHGI
QRGDIDAMIS SAKSMVRKAN DITDEVLDGL NPIQTDVERI KDTYGRTQNE DFKKALTDAD
NSVNKLTNKL PDLWRKIESI NQQLLPLGNI SDNMDRIREL IQQARDAASK VAVPMRFNGK
SGVEVRLPND LEDLKGYTSL SLFLQRPNSR ENGGTENMFV MYLGNKDASR DYIGMAVVDG
QLTCVYNLGD REAELQVDQI LTKSETKEAV MDRVKFQRIY QFARLNYTKG ATSSKPETPG
VYDMDGRNSN TLLNLDPENV VFYVGGYPPD FKLPSRLSFP PYKGCIELDD LNENVLSLYN
FKKTFNLNTT EVEPCRRRKE ESDKNYFEGT GYARVPTQPH APIPTFGQTI QTTVDRGLLF
FAENGDRFIS LNIEDGKLMV RYKLNSELPK ERGVGDAINN GRDHSIQIKI GKLQKRMWIN
VDVQNTIIDG EVFDFSTYYL GGIPIAIRER FNISTPAFRG CMKNLKKTSG VVRLNDTVGV
TKKCSEDWKL VRSASFSRGG QLSFTDLGLP PTDHLQASFG FQTFQPSGIL LDHQTWTRNL
QVTLEDGYIE LSTSDSGGPI FKSPQTYMDG LLHYVSVISD NSGLRLLIDD QLLRNSKRLK
HISSSRQSLR LGGSNFEGCI SNVFVQRLSL SPEVLDLTSN SLKRDVSLGG CSLNKPPFLM
LLKGSTRFNK TKTFRINQLL QDTPVASPRS VKVWQDACSP LPKTQANHGA LQFGDIPTSH
LLFKLPQELL KPRSQFAVDM QTTSSRGLVF HTGTKNSFMA LYLSKGRLVF ALGTDGKKLR
IKSKEKCNDG KWHTVVFGHD GEKGRLVVDG LRAREGSLPG NSTISIRAPV YLGSPPSGKP
KSLPTNSFVG CLKNFQLDSK PLYTPSSSFG VSSCLGGPLE KGIYFSEEGG HVVLAHSVLL
GPEFKLVFSI RPRSLTGILI HIGSQPGKHL CVYLEAGKVT ASMDSGAGGT STSVTPKQSL
CDGQWHSVAV TIKQHILHLE LDTDSSYTAG QIPFPPASTQ EPLHLGGAPA NLTTLRIPVW
KSFFGCLRNI HVNHIPVPVT EALEVQGPVS LNGCPDQ*

Mutated AA sequence

MAAAARPRGR ALGPVLPPTP LLLLVLRVLP ACGATARDPG AAAGLSLHPT YFNLAEAARI
WATATCGERG PGEGRPQPEL YCKLVGGPTA PGSGHTIQGQ FCDYCNSEDP RKAHPVTNAI
DGSERWWQSP PLSSGTQYNR VNLTLDLGQL FHVAYILIKF ANSPRPDLWV LERSVDFGST
YSPWQYFAHS KVDCLKEFGR EANMAVTRDD DVLCVTEYSR IVPLENGEVV VSLINGRPGA
KNFTFSHTLR EFTKATNIRL RFLRTNTLLG HLISKAQRDP TVTRRYYYSI KDISIGGQCV
CNGHAEVCNI NNPEKLFRCE CQHHTCGETC DRCCTGYNQR RWRPAAWEQS HECEACNCHG
HASNCYYDPD VERQQASLNT QGIYAGGGVC INCQHNTAGV NCEQCAKGYY RPYGVPVDAP
DGCIPCSCDP EHADGCEQGS GRCHCKPNFH GDNCEKCAIG YYNFPFCLRI PIFPVSTPSS
EDPVAGDIKG CDCNLEGVLP EICDAHGRCL CRPGVEGPRC DTCRSGFYSF PICQACWCSA
LGSYQMPCSS VTGQCECRPG VTGQRCDRCL SGAYDFPHCQ GSSSACDPAG TINSNLGYCQ
CKLHVEGPTC SRCKLLYWNL DKENPSGCSE CKCHKAGTVS GTGECRQGDG DCHCKSHVGG
DSCDTCEDGY FALEKSNYFG CQGCQCDIGG ALSSMCSGPS GVCQCREHVV GKVCQRPENN
YYFPDLHHMK YEIEDGSTPN GRDLRFGFDP LAFPEFSWRG YAQMTSVQND VRITLNVGKS
SGSLFRVILR YVNPGTEAVS GHITIYPSWG AAQSKEIIFL PSKEPAFVTV PGNGFADPFS
ITPGIWVACI KAEGVLLDYL VLLPRDYYEA SVLQLPVTEP CAYAGPPQEN CLLYQHLPVT
RFPCTLACEA RHFLLDGEPR PVAVRQPTPA HPVMVDLSGR EVELHLRLRI PQVGHYVVVV
EYSTEAAQLF VVDVNVKSSG SVLAGQVNIY SCNYSVLCRS AVIDHMSRIA MYELLADADI
QLKGHMARFL LHQVCIIPIE EFSAEYVRPQ VHCIASYGRF VNQSATCVSL AHETPPTALI
LDVLSGRPFP HLPQQSSPSV DVLPGVTLKA PQNQVTLRGR VPHLGRYVFV IHFYQAAHPT
FPAQVSVDGG WPRAGSFHAS FCPHVLGCRD QVIAEGQIEF DISEPEVAAT VKVPEGKSLV
LVRVLVVPAE NYDYQILHKK SMDKSLEFIT NCGKNSFYLD PQTASRFCKN SARSLVAFYH
KGALPCECHP TGATGPHCSP EGGQCPCQPN VIGRQCTRCA TGHYGFPRCK PCSCGRRLCE
EMTGQCRCPP RTVRPQCEVC ETHSFSFHPM AGCEGCNCSR RGTIEAAMPE CDRDSGQCRC
KPRITGRQCD RCASGFYRFP ECVPCNCNRD GTEPGVCDPG TGACLCKENV EGTECNVCRE
GSFHLDPANL KGCTSCFCFG VNNQCHSSHK RRTKFVDMLG WHLETADRVD IPVSFNPGSN
SMVADLQELP ATIHSASWVA PTSYLGDKVS SYGGYLTYQA KSFGLPGDMV LLEKKPDVQL
TGQHMSIIYE ETNTPRPDRL HHGRVHVVEG NFRHASSRAP VSREELMTVL SRLADVRIQG
LYFTETQRLT LSEVGLEEAS DTGSGRIALA VEICACPPAY AGDSCQGCSP GYYRDHKGLY
TGRCVPCNCN GHSNQCQDGS GICVNCQHNT AGEHCERCQE GYYGNAVHGS CRACPCPHTN
SFATGCVVNG GDVRCSCKAG YTGTQCERCA PGYFGNPQKF GGSCQPCSCN SNGQLGSCHP
LTGDCINQEP KDSSPAEECD DCDSCVMTLL NDLATMGEQL RLVKSQLQGL SASAGLLEQM
RHMETQAKDL RNQLLNYRSA ISNHGSKIEG LERELTDLNQ EFETLQEKAQ VNSRKAQTLN
NNVNRATQSA KELDVKIKNV IRNVHMLNRI RTWQKTHQGE NNGLANSIRD SLNEYEAKLS
DLRARLQEAA AQAKQANGLN QENERALGAI QRQVKEINSL QSDFTKYLTT ADSSLLQTNI
ALQLMEKSQK EYEKLAASLN EARQELSDKV RELSRSAGKT SLVEEAEKHA RSLQELAKQL
EEIKRNASGD ELVRCAVDAA TAYENILNAI KAAEDAANRA ASASESALQT VIKEDLPRKA
KTLSSNSDKL LNEAKMTQKK LKQEVSPALN NLQQTLNIVT VQKEVIDTNL TTLRDGLHGI
QRGDIDAMIS SAKSMVRKAN DITDEVLDGL NPIQTDVERI KDTYGRTQNE DFKKALTDAD
NSVNKLTNKL PDLWRKIESI NQQLLPLGNI SDNMDRIREL IQQARDAASK VAVPMRFNGK
SGVEVRLPND LEDLKGYTSL SLFLQRPNSR ENGGTENMFV MYLGNKDASR DYIGMAVVDG
QLTCVYNLGD REAELQVDQI LTKSETKEAV MDRVKFQRIY QFARLNYTKG ATSSKPETPG
VYDMDGRNSN TLLNLDPENV VFYVGGYPPD FKLPSRLSFP PYKGCIELDD LNENVLSLYN
FKKTFNLNTT EVEPCRRRKE ESDKNYFEGT GYARVPTQPH APIPTFGQTI QTTVDRGLLF
FAENGDRFIS LNIEDGKLMV RYKLNSELPK ERGVGDAINN GRDHSIQIKI GKLQKRMWIN
VDVQNTIIDG EVFDFSTYYL GGIPIAIRER FNISTPAFRG CMKNLKKTSG VVRLNDTVGV
TKKCSEDWKL VRSASFSRGG QLSFTDLGLP PTDHLQASFG FQTFQPSGIL LDHQTWTRNL
QVTLEDGYIE LSTSDSGGPI FKSPQTYMDG LLHYVSVISD NSGLRLLIDD QLLRNSKRLK
HISSSRQSLR LGGSNFEGCI SNVFVQRLSL SPEVLDLTSN SLKRDVSLGG CSLNKPPFLM
LLKGSTRFNK TKTFCINQLL QDTPVASPRS VKVWQDACSP LPKTQANHGA LQFGDIPTSH
LLFKLPQELL KPRSQFAVDM QTTSSRGLVF HTGTKNSFMA LYLSKGRLVF ALGTDGKKLR
IKSKEKCNDG KWHTVVFGHD GEKGRLVVDG LRAREGSLPG NSTISIRAPV YLGSPPSGKP
KSLPTNSFVG CLKNFQLDSK PLYTPSSSFG VSSCLGGPLE KGIYFSEEGG HVVLAHSVLL
GPEFKLVFSI RPRSLTGILI HIGSQPGKHL CVYLEAGKVT ASMDSGAGGT STSVTPKQSL
CDGQWHSVAV TIKQHILHLE LDTDSSYTAG QIPFPPASTQ EPLHLGGAPA NLTTLRIPVW
KSFFGCLRNI HVNHIPVPVT EALEVQGPVS LNGCPDQ*

Position of stopcodon in wt / mu CDS

9834 / 9834

Position (AA) of stopcodon in wt / mu AA sequence

3278 / 3278

Position of stopcodon in wt / mu cDNA

9834 / 9834

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

9688

Theoretical NMD boundary in CDS

9637

Length of CDS

9834

Coding sequence (CDS) position

8683

cDNA position

8683

gDNA position

244472

Chromosomal position

23933924

Speed

0.06 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

18:23933924C>T_3_ENST00000269217

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 36|64 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr18:23933924C>T (GRCh38)

Gene symbol

LAMA3

Gene constraints

LOEUF: 0.71, LOF (oe): 0.60, misssense (oe): 0.88, synonymous (oe): 0.86 ? (gnomAD)

Ensembl transcript ID

ENST00000269217.11

Genbank transcript ID

NM_000227 (exact from MANE)

UniProt / AlphaMissense peptide

LAMA3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.4024C>T
g.244472C>T

AA changes

AAE:	R1342C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs61752346
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	10	3959	3969

Protein conservation

Species	Match	AA	Alignment
Human		1342	G	S	T	R	F	N	K	T	K	T	F	R	I	N	Q	L	L	Q	D	T	P	V	A	S
mutated	not conserved	1342	G	S	T	R	F	N	K	T	K	T	F	C	I	N	Q	L	L	Q	D	T	P	V	A
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
36	3333	CHAIN		lost
1266	1465	REGION		lost
1312	1355	DOMAIN	Laminin EGF-like	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.026	0
	-0.284	0
(flanking)	-1.257	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

18

Strand

1

Original gDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGGTAAGTGTC

Altered gDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGGTAAGTGTC

Original cDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGCTGTTGCAG

Altered cDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGCTGTTGCAG

Wildtype AA sequence

MPPAVRRSAC SMGWLWIFGA ALGQCLGYSS QQQRVPFLQP PGQSQLQASY VEFRPSQGCS
PGYYRDHKGL YTGRCVPCNC NGHSNQCQDG SGICVNCQHN TAGEHCERCQ EGYYGNAVHG
SCRACPCPHT NSFATGCVVN GGDVRCSCKA GYTGTQCERC APGYFGNPQK FGGSCQPCSC
NSNGQLGSCH PLTGDCINQE PKDSSPAEEC DDCDSCVMTL LNDLATMGEQ LRLVKSQLQG
LSASAGLLEQ MRHMETQAKD LRNQLLNYRS AISNHGSKIE GLERELTDLN QEFETLQEKA
QVNSRKAQTL NNNVNRATQS AKELDVKIKN VIRNVHILLK QISGTDGEGN NVPSGDFSRE
WAEAQRMMRE LRNRNFGKHL REAEADKRES QLLLNRIRTW QKTHQGENNG LANSIRDSLN
EYEAKLSDLR ARLQEAAAQA KQANGLNQEN ERALGAIQRQ VKEINSLQSD FTKYLTTADS
SLLQTNIALQ LMEKSQKEYE KLAASLNEAR QELSDKVREL SRSAGKTSLV EEAEKHARSL
QELAKQLEEI KRNASGDELV RCAVDAATAY ENILNAIKAA EDAANRAASA SESALQTVIK
EDLPRKAKTL SSNSDKLLNE AKMTQKKLKQ EVSPALNNLQ QTLNIVTVQK EVIDTNLTTL
RDGLHGIQRG DIDAMISSAK SMVRKANDIT DEVLDGLNPI QTDVERIKDT YGRTQNEDFK
KALTDADNSV NKLTNKLPDL WRKIESINQQ LLPLGNISDN MDRIRELIQQ ARDAASKVAV
PMRFNGKSGV EVRLPNDLED LKGYTSLSLF LQRPNSRENG GTENMFVMYL GNKDASRDYI
GMAVVDGQLT CVYNLGDREA ELQVDQILTK SETKEAVMDR VKFQRIYQFA RLNYTKGATS
SKPETPGVYD MDGRNSNTLL NLDPENVVFY VGGYPPDFKL PSRLSFPPYK GCIELDDLNE
NVLSLYNFKK TFNLNTTEVE PCRRRKEESD KNYFEGTGYA RVPTQPHAPI PTFGQTIQTT
VDRGLLFFAE NGDRFISLNI EDGKLMVRYK LNSELPKERG VGDAINNGRD HSIQIKIGKL
QKRMWINVDV QNTIIDGEVF DFSTYYLGGI PIAIRERFNI STPAFRGCMK NLKKTSGVVR
LNDTVGVTKK CSEDWKLVRS ASFSRGGQLS FTDLGLPPTD HLQASFGFQT FQPSGILLDH
QTWTRNLQVT LEDGYIELST SDSGGPIFKS PQTYMDGLLH YVSVISDNSG LRLLIDDQLL
RNSKRLKHIS SSRQSLRLGG SNFEGCISNV FVQRLSLSPE VLDLTSNSLK RDVSLGGCSL
NKPPFLMLLK GSTRFNKTKT FRINQLLQDT PVASPRSVKV WQDACSPLPK TQANHGALQF
GDIPTSHLLF KLPQELLKPR SQFAVDMQTT SSRGLVFHTG TKNSFMALYL SKGRLVFALG
TDGKKLRIKS KEKCNDGKWH TVVFGHDGEK GRLVVDGLRA REGSLPGNST ISIRAPVYLG
SPPSGKPKSL PTNSFVGCLK NFQLDSKPLY TPSSSFGVSS CLGGPLEKGI YFSEEGGHVV
LAHSVLLGPE FKLVFSIRPR SLTGILIHIG SQPGKHLCVY LEAGKVTASM DSGAGGTSTS
VTPKQSLCDG QWHSVAVTIK QHILHLELDT DSSYTAGQIP FPPASTQEPL HLGGAPANLT
TLRIPVWKSF FGCLRNIHVN HIPVPVTEAL EVQGPVSLNG CPDQ*

Mutated AA sequence

MPPAVRRSAC SMGWLWIFGA ALGQCLGYSS QQQRVPFLQP PGQSQLQASY VEFRPSQGCS
PGYYRDHKGL YTGRCVPCNC NGHSNQCQDG SGICVNCQHN TAGEHCERCQ EGYYGNAVHG
SCRACPCPHT NSFATGCVVN GGDVRCSCKA GYTGTQCERC APGYFGNPQK FGGSCQPCSC
NSNGQLGSCH PLTGDCINQE PKDSSPAEEC DDCDSCVMTL LNDLATMGEQ LRLVKSQLQG
LSASAGLLEQ MRHMETQAKD LRNQLLNYRS AISNHGSKIE GLERELTDLN QEFETLQEKA
QVNSRKAQTL NNNVNRATQS AKELDVKIKN VIRNVHILLK QISGTDGEGN NVPSGDFSRE
WAEAQRMMRE LRNRNFGKHL REAEADKRES QLLLNRIRTW QKTHQGENNG LANSIRDSLN
EYEAKLSDLR ARLQEAAAQA KQANGLNQEN ERALGAIQRQ VKEINSLQSD FTKYLTTADS
SLLQTNIALQ LMEKSQKEYE KLAASLNEAR QELSDKVREL SRSAGKTSLV EEAEKHARSL
QELAKQLEEI KRNASGDELV RCAVDAATAY ENILNAIKAA EDAANRAASA SESALQTVIK
EDLPRKAKTL SSNSDKLLNE AKMTQKKLKQ EVSPALNNLQ QTLNIVTVQK EVIDTNLTTL
RDGLHGIQRG DIDAMISSAK SMVRKANDIT DEVLDGLNPI QTDVERIKDT YGRTQNEDFK
KALTDADNSV NKLTNKLPDL WRKIESINQQ LLPLGNISDN MDRIRELIQQ ARDAASKVAV
PMRFNGKSGV EVRLPNDLED LKGYTSLSLF LQRPNSRENG GTENMFVMYL GNKDASRDYI
GMAVVDGQLT CVYNLGDREA ELQVDQILTK SETKEAVMDR VKFQRIYQFA RLNYTKGATS
SKPETPGVYD MDGRNSNTLL NLDPENVVFY VGGYPPDFKL PSRLSFPPYK GCIELDDLNE
NVLSLYNFKK TFNLNTTEVE PCRRRKEESD KNYFEGTGYA RVPTQPHAPI PTFGQTIQTT
VDRGLLFFAE NGDRFISLNI EDGKLMVRYK LNSELPKERG VGDAINNGRD HSIQIKIGKL
QKRMWINVDV QNTIIDGEVF DFSTYYLGGI PIAIRERFNI STPAFRGCMK NLKKTSGVVR
LNDTVGVTKK CSEDWKLVRS ASFSRGGQLS FTDLGLPPTD HLQASFGFQT FQPSGILLDH
QTWTRNLQVT LEDGYIELST SDSGGPIFKS PQTYMDGLLH YVSVISDNSG LRLLIDDQLL
RNSKRLKHIS SSRQSLRLGG SNFEGCISNV FVQRLSLSPE VLDLTSNSLK RDVSLGGCSL
NKPPFLMLLK GSTRFNKTKT FCINQLLQDT PVASPRSVKV WQDACSPLPK TQANHGALQF
GDIPTSHLLF KLPQELLKPR SQFAVDMQTT SSRGLVFHTG TKNSFMALYL SKGRLVFALG
TDGKKLRIKS KEKCNDGKWH TVVFGHDGEK GRLVVDGLRA REGSLPGNST ISIRAPVYLG
SPPSGKPKSL PTNSFVGCLK NFQLDSKPLY TPSSSFGVSS CLGGPLEKGI YFSEEGGHVV
LAHSVLLGPE FKLVFSIRPR SLTGILIHIG SQPGKHLCVY LEAGKVTASM DSGAGGTSTS
VTPKQSLCDG QWHSVAVTIK QHILHLELDT DSSYTAGQIP FPPASTQEPL HLGGAPANLT
TLRIPVWKSF FGCLRNIHVN HIPVPVTEAL EVQGPVSLNG CPDQ*

Position of stopcodon in wt / mu CDS

5175 / 5175

Position (AA) of stopcodon in wt / mu AA sequence

1725 / 1725

Position of stopcodon in wt / mu cDNA

5200 / 5200

Position of start ATG in wt / mu cDNA

26 / 26

Last intron/exon boundary

5054

Theoretical NMD boundary in CDS

4978

Length of CDS

5175

Coding sequence (CDS) position

4024

cDNA position

4049

gDNA position

244472

Chromosomal position

23933924

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

Back to summary table

MutationT@ster 2025

Variant:

18:23933924C>T_4_ENST00000587184

Back to summary table

Prediction:

BenignPermalink

Summary:

Amino acid sequence changed
Heterozygous in gnomAD
Protein features (might be) affected

Model: simple_aae
Tree vote: 37|63 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr18:23933924C>T (GRCh38)

Gene symbol

LAMA3

Gene constraints

LOEUF: 0.67, LOF (oe): 0.56, misssense (oe): 0.88, synonymous (oe): 0.87 ? (gnomAD)

Ensembl transcript ID

ENST00000587184.5

Genbank transcript ID

NM_001127718 (by similarity)

UniProt / AlphaMissense peptide

LAMA3_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.3856C>T
g.244472C>T

AA changes

AAE:	R1286C	?
Score:	180

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs61752346
gnomAD	homozygous (T/T)	heterozygous	allele carriers
	10	3959	3969

Protein conservation

Species	Match	AA	Alignment
Human		1286	G	S	T	R	F	N	K	T	K	T	F	R	I	N	Q	L	L	Q	D	T	P	V	A	S
mutated	not conserved	1286	G	S	T	R	F	N	K	T	K	T	F	C	I	N	Q	L	L	Q	D	T	P	V	A
Ptroglodytes	no homologue
Mmulatta	no homologue
Fcatus	no homologue
Mmusculus	no homologue
Ggallus	no homologue
Trubripes	no homologue
Drerio	no homologue
Dmelanogaster	no homologue
Celegans	no homologue
Xtropicalis	no homologue

Protein features

Start (aa)	End (aa)	Feature	Details
36	3333	CHAIN		lost
1266	1311	DOMAIN	Laminin EGF-like	lost
1266	1465	REGION		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.026	0
	-0.284	0
(flanking)	-1.257	0

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

12

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

18

Strand

1

Original gDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGGTAAGTGTC

Altered gDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGGTAAGTGTC

Original cDNA sequence snippet

TTAACAAGACCAAGACTTTTCGTATCAACCAGCTGTTGCAG

Altered cDNA sequence snippet

TTAACAAGACCAAGACTTTTTGTATCAACCAGCTGTTGCAG

Wildtype AA sequence

MPPAVRRSAC SMGWLWIFGA ALGQCLGYSS QQQRVPFLQP PGQSQLQASY VEFRPSQGCS
PGYYRDHKGL YTGRCVPCNC NGHSNQCQDG SGICVNCQHN TAGEHCERCQ EGYYGNAVHG
SCRACPCPHT NSFATGCVVN GGDVRCSCKA GYTGTQCERC APGYFGNPQK FGGSCQPCSC
NSNGQLGSCH PLTGDCINQE PKDSSPAEEC DDCDSCVMTL LNDLATMGEQ LRLVKSQLQG
LSASAGLLEQ MRHMETQAKD LRNQLLNYRS AISNHGSKIE GLERELTDLN QEFETLQEKA
QVNSRKAQTL NNNVNRATQS AKELDVKIKN VIRNVHMLNR IRTWQKTHQG ENNGLANSIR
DSLNEYEAKL SDLRARLQEA AAQAKQANGL NQENERALGA IQRQVKEINS LQSDFTKYLT
TADSSLLQTN IALQLMEKSQ KEYEKLAASL NEARQELSDK VRELSRSAGK TSLVEEAEKH
ARSLQELAKQ LEEIKRNASG DELVRCAVDA ATAYENILNA IKAAEDAANR AASASESALQ
TVIKEDLPRK AKTLSSNSDK LLNEAKMTQK KLKQEVSPAL NNLQQTLNIV TVQKEVIDTN
LTTLRDGLHG IQRGDIDAMI SSAKSMVRKA NDITDEVLDG LNPIQTDVER IKDTYGRTQN
EDFKKALTDA DNSVNKLTNK LPDLWRKIES INQQLLPLGN ISDNMDRIRE LIQQARDAAS
KVAVPMRFNG KSGVEVRLPN DLEDLKGYTS LSLFLQRPNS RENGGTENMF VMYLGNKDAS
RDYIGMAVVD GQLTCVYNLG DREAELQVDQ ILTKSETKEA VMDRVKFQRI YQFARLNYTK
GATSSKPETP GVYDMDGRNS NTLLNLDPEN VVFYVGGYPP DFKLPSRLSF PPYKGCIELD
DLNENVLSLY NFKKTFNLNT TEVEPCRRRK EESDKNYFEG TGYARVPTQP HAPIPTFGQT
IQTTVDRGLL FFAENGDRFI SLNIEDGKLM VRYKLNSELP KERGVGDAIN NGRDHSIQIK
IGKLQKRMWI NVDVQNTIID GEVFDFSTYY LGGIPIAIRE RFNISTPAFR GCMKNLKKTS
GVVRLNDTVG VTKKCSEDWK LVRSASFSRG GQLSFTDLGL PPTDHLQASF GFQTFQPSGI
LLDHQTWTRN LQVTLEDGYI ELSTSDSGGP IFKSPQTYMD GLLHYVSVIS DNSGLRLLID
DQLLRNSKRL KHISSSRQSL RLGGSNFEGC ISNVFVQRLS LSPEVLDLTS NSLKRDVSLG
GCSLNKPPFL MLLKGSTRFN KTKTFRINQL LQDTPVASPR SVKVWQDACS PLPKTQANHG
ALQFGDIPTS HLLFKLPQEL LKPRSQFAVD MQTTSSRGLV FHTGTKNSFM ALYLSKGRLV
FALGTDGKKL RIKSKEKCND GKWHTVVFGH DGEKGRLVVD GLRAREGSLP GNSTISIRAP
VYLGSPPSGK PKSLPTNSFV GCLKNFQLDS KPLYTPSSSF GVSSCLGGPL EKGIYFSEEG
GHVVLAHSVL LGPEFKLVFS IRPRSLTGIL IHIGSQPGKH LCVYLEAGKV TASMDSGAGG
TSTSVTPKQS LCDGQWHSVA VTIKQHILHL ELDTDSSYTA GQIPFPPAST QEPLHLGGAP
ANLTTLRIPV WKSFFGCLRN IHVNHIPVPV TEALEVQGPV SLNGCPDQ*

Mutated AA sequence

MPPAVRRSAC SMGWLWIFGA ALGQCLGYSS QQQRVPFLQP PGQSQLQASY VEFRPSQGCS
PGYYRDHKGL YTGRCVPCNC NGHSNQCQDG SGICVNCQHN TAGEHCERCQ EGYYGNAVHG
SCRACPCPHT NSFATGCVVN GGDVRCSCKA GYTGTQCERC APGYFGNPQK FGGSCQPCSC
NSNGQLGSCH PLTGDCINQE PKDSSPAEEC DDCDSCVMTL LNDLATMGEQ LRLVKSQLQG
LSASAGLLEQ MRHMETQAKD LRNQLLNYRS AISNHGSKIE GLERELTDLN QEFETLQEKA
QVNSRKAQTL NNNVNRATQS AKELDVKIKN VIRNVHMLNR IRTWQKTHQG ENNGLANSIR
DSLNEYEAKL SDLRARLQEA AAQAKQANGL NQENERALGA IQRQVKEINS LQSDFTKYLT
TADSSLLQTN IALQLMEKSQ KEYEKLAASL NEARQELSDK VRELSRSAGK TSLVEEAEKH
ARSLQELAKQ LEEIKRNASG DELVRCAVDA ATAYENILNA IKAAEDAANR AASASESALQ
TVIKEDLPRK AKTLSSNSDK LLNEAKMTQK KLKQEVSPAL NNLQQTLNIV TVQKEVIDTN
LTTLRDGLHG IQRGDIDAMI SSAKSMVRKA NDITDEVLDG LNPIQTDVER IKDTYGRTQN
EDFKKALTDA DNSVNKLTNK LPDLWRKIES INQQLLPLGN ISDNMDRIRE LIQQARDAAS
KVAVPMRFNG KSGVEVRLPN DLEDLKGYTS LSLFLQRPNS RENGGTENMF VMYLGNKDAS
RDYIGMAVVD GQLTCVYNLG DREAELQVDQ ILTKSETKEA VMDRVKFQRI YQFARLNYTK
GATSSKPETP GVYDMDGRNS NTLLNLDPEN VVFYVGGYPP DFKLPSRLSF PPYKGCIELD
DLNENVLSLY NFKKTFNLNT TEVEPCRRRK EESDKNYFEG TGYARVPTQP HAPIPTFGQT
IQTTVDRGLL FFAENGDRFI SLNIEDGKLM VRYKLNSELP KERGVGDAIN NGRDHSIQIK
IGKLQKRMWI NVDVQNTIID GEVFDFSTYY LGGIPIAIRE RFNISTPAFR GCMKNLKKTS
GVVRLNDTVG VTKKCSEDWK LVRSASFSRG GQLSFTDLGL PPTDHLQASF GFQTFQPSGI
LLDHQTWTRN LQVTLEDGYI ELSTSDSGGP IFKSPQTYMD GLLHYVSVIS DNSGLRLLID
DQLLRNSKRL KHISSSRQSL RLGGSNFEGC ISNVFVQRLS LSPEVLDLTS NSLKRDVSLG
GCSLNKPPFL MLLKGSTRFN KTKTFCINQL LQDTPVASPR SVKVWQDACS PLPKTQANHG
ALQFGDIPTS HLLFKLPQEL LKPRSQFAVD MQTTSSRGLV FHTGTKNSFM ALYLSKGRLV
FALGTDGKKL RIKSKEKCND GKWHTVVFGH DGEKGRLVVD GLRAREGSLP GNSTISIRAP
VYLGSPPSGK PKSLPTNSFV GCLKNFQLDS KPLYTPSSSF GVSSCLGGPL EKGIYFSEEG
GHVVLAHSVL LGPEFKLVFS IRPRSLTGIL IHIGSQPGKH LCVYLEAGKV TASMDSGAGG
TSTSVTPKQS LCDGQWHSVA VTIKQHILHL ELDTDSSYTA GQIPFPPAST QEPLHLGGAP
ANLTTLRIPV WKSFFGCLRN IHVNHIPVPV TEALEVQGPV SLNGCPDQ*

Position of stopcodon in wt / mu CDS

5007 / 5007

Position (AA) of stopcodon in wt / mu AA sequence

1669 / 1669

Position of stopcodon in wt / mu cDNA

5007 / 5007

Position of start ATG in wt / mu cDNA

1 / 1

Last intron/exon boundary

4861

Theoretical NMD boundary in CDS

4810

Length of CDS

5007

Coding sequence (CDS) position

3856

cDNA position

3856

gDNA position

244472

Chromosomal position

23933924

Speed

0.05 s

All positions are in basepairs (bp) if not explicitly stated differently. cDNA/gDNA/chromosomal position: Ins/del are shown as 'last normal base / first normal base'.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project

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