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: ENST00000648685
Querying Taster for transcript #2: ENST00000544665
MT speed 0.2 s - this script 2.625884 s

Transcript summary:

Permalink

Transcript	Gene symbol	Prediction	Tree vote	Model	Prediction problem	Splice site change	Known ClinVar disease mutation	Potential ClinVar disease mutation	Amino acid changes	Variant type	dbSNP ID	Protein length	Features at a glance
ENST00000544665(MANE Select)	ITGAM	Benign	14\|86	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected
ENST00000648685	ITGAM	Benign	25\|75	simple_aae		No				Single base exchange		Normal	Amino acid sequence changed Homozygous in gnomAD Protein features (might be) affected

MutationT@ster 2025

Variant:

16:31265490G>A_2_ENST00000544665

Back to summary table

Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 14|86 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:31265490G>A (GRCh38)

Gene symbol

ITGAM

Gene constraints

LOEUF: 0.68, LOF (oe): 0.55, misssense (oe): 0.90, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000544665.9

Genbank transcript ID

NM_000632 (exact from MANE)

UniProt / AlphaMissense peptide

ITAM_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.230G>A
g.5524G>A

AA changes

AAE:	R77H	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1143679
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	8785	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		77	C	D	Y	S	T	G	S	C	E	P	I	R	L	Q	V	P	V	E	A	V	N	M	S	L
mutated	not conserved	77	C	D	Y	S	T	G	S	C	E	P	I	H	L	Q	V	P	V	E	A	V	N	M	S
Ptroglodytes	all identical	77	C	D	Y	S	T	G	S	C	E	P	I	R	L	Q	V	P	V	E	A	V	N	M	S
Mmulatta	all identical	197	C	D	Y	S	I	G	S	C	E	P	I	R	L	Q	I	P	E	E	A	V	N	M	S
Fcatus	not conserved	84	C	D	Y	S	T	G	K	C	E	P	I	S	L	E	V	P	L	E	A	V	N	M	S
Mmusculus	not conserved	77	C	D	Y	S	T	S	R	C	H	P	I	P	L	Q	V	P	P	E	A	V	N	M	S
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
17	1104	TOPO_DOM	Extracellular	lost
17	1152	CHAIN		lost
76	135	REPEAT	FG-GAP	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.236	0
	-1.519	0
(flanking)	-0.049	0.001

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

16

Strand

1

Original gDNA sequence snippet

AGGCTCATGCGAGCCCATCCGCCTGCAGGGTGAGTCACTGC

Altered gDNA sequence snippet

AGGCTCATGCGAGCCCATCCACCTGCAGGGTGAGTCACTGC

Original cDNA sequence snippet

AGGCTCATGCGAGCCCATCCGCCTGCAGGTCCCCGTGGAGG

Altered cDNA sequence snippet

AGGCTCATGCGAGCCCATCCACCTGCAGGTCCCCGTGGAGG

Wildtype AA sequence

MALRVLLLTA LTLCHGFNLD TENAMTFQEN ARGFGQSVVQ LQGSRVVVGA PQEIVAANQR
GSLYQCDYST GSCEPIRLQV PVEAVNMSLG LSLAATTSPP QLLACGPTVH QTCSENTYVK
GLCFLFGSNL RQQPQKFPEA LRGCPQEDSD IAFLIDGSGS IIPHDFRRMK EFVSTVMEQL
KKSKTLFSLM QYSEEFRIHF TFKEFQNNPN PRSLVKPITQ LLGRTHTATG IRKVVRELFN
ITNGARKNAF KILVVITDGE KFGDPLGYED VIPEADREGV IRYVIGVGDA FRSEKSRQEL
NTIASKPPRD HVFQVNNFEA LKTIQNQLRE KIFAIEGTQT GSSSSFEHEM SQEGFSAAIT
SNGPLLSTVG SYDWAGGVFL YTSKEKSTFI NMTRVDSDMN DAYLGYAAAI ILRNRVQSLV
LGAPRYQHIG LVAMFRQNTG MWESNANVKG TQIGAYFGAS LCSVDVDSNG STDLVLIGAP
HYYEQTRGGQ VSVCPLPRGR ARWQCDAVLY GEQGQPWGRF GAALTVLGDV NGDKLTDVAI
GAPGEEDNRG AVYLFHGTSG SGISPSHSQR IAGSKLSPRL QYFGQSLSGG QDLTMDGLVD
LTVGAQGHVL LLRSQPVLRV KAIMEFNPRE VARNVFECND QVVKGKEAGE VRVCLHVQKS
TRDRLREGQI QSVVTYDLAL DSGRPHSRAV FNETKNSTRR QTQVLGLTQT CETLKLQLPN
CIEDPVSPIV LRLNFSLVGT PLSAFGNLRP VLAEDAQRLF TALFPFEKNC GNDNICQDDL
SITFSFMSLD CLVVGGPREF NVTVTVRNDG EDSYRTQVTF FFPLDLSYRK VSTLQNQRSQ
RSWRLACESA SSTEVSGALK STSCSINHPI FPENSEVTFN ITFDVDSKAS LGNKLLLKAN
VTSENNMPRT NKTEFQLELP VKYAVYMVVT SHGVSTKYLN FTASENTSRV MQHQYQVSNL
GQRSLPISLV FLVPVRLNQT VIWDRPQVTF SENLSSTCHT KERLPSHSDF LAELRKAPVV
NCSIAVCQRI QCDIPFFGIQ EEFNATLKGN LSFDWYIKTS HNHLLIVSTA EILFNDSVFT
LLPGQGAFVR SQTETKVEPF EVPNPLPLIV GSSVGGLLLL ALITAALYKL GFFKRQYKDM
MSEGGPPGAE PQ*

Mutated AA sequence

MALRVLLLTA LTLCHGFNLD TENAMTFQEN ARGFGQSVVQ LQGSRVVVGA PQEIVAANQR
GSLYQCDYST GSCEPIHLQV PVEAVNMSLG LSLAATTSPP QLLACGPTVH QTCSENTYVK
GLCFLFGSNL RQQPQKFPEA LRGCPQEDSD IAFLIDGSGS IIPHDFRRMK EFVSTVMEQL
KKSKTLFSLM QYSEEFRIHF TFKEFQNNPN PRSLVKPITQ LLGRTHTATG IRKVVRELFN
ITNGARKNAF KILVVITDGE KFGDPLGYED VIPEADREGV IRYVIGVGDA FRSEKSRQEL
NTIASKPPRD HVFQVNNFEA LKTIQNQLRE KIFAIEGTQT GSSSSFEHEM SQEGFSAAIT
SNGPLLSTVG SYDWAGGVFL YTSKEKSTFI NMTRVDSDMN DAYLGYAAAI ILRNRVQSLV
LGAPRYQHIG LVAMFRQNTG MWESNANVKG TQIGAYFGAS LCSVDVDSNG STDLVLIGAP
HYYEQTRGGQ VSVCPLPRGR ARWQCDAVLY GEQGQPWGRF GAALTVLGDV NGDKLTDVAI
GAPGEEDNRG AVYLFHGTSG SGISPSHSQR IAGSKLSPRL QYFGQSLSGG QDLTMDGLVD
LTVGAQGHVL LLRSQPVLRV KAIMEFNPRE VARNVFECND QVVKGKEAGE VRVCLHVQKS
TRDRLREGQI QSVVTYDLAL DSGRPHSRAV FNETKNSTRR QTQVLGLTQT CETLKLQLPN
CIEDPVSPIV LRLNFSLVGT PLSAFGNLRP VLAEDAQRLF TALFPFEKNC GNDNICQDDL
SITFSFMSLD CLVVGGPREF NVTVTVRNDG EDSYRTQVTF FFPLDLSYRK VSTLQNQRSQ
RSWRLACESA SSTEVSGALK STSCSINHPI FPENSEVTFN ITFDVDSKAS LGNKLLLKAN
VTSENNMPRT NKTEFQLELP VKYAVYMVVT SHGVSTKYLN FTASENTSRV MQHQYQVSNL
GQRSLPISLV FLVPVRLNQT VIWDRPQVTF SENLSSTCHT KERLPSHSDF LAELRKAPVV
NCSIAVCQRI QCDIPFFGIQ EEFNATLKGN LSFDWYIKTS HNHLLIVSTA EILFNDSVFT
LLPGQGAFVR SQTETKVEPF EVPNPLPLIV GSSVGGLLLL ALITAALYKL GFFKRQYKDM
MSEGGPPGAE PQ*

Position of stopcodon in wt / mu CDS

3459 / 3459

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

1153 / 1153

Position of stopcodon in wt / mu cDNA

3549 / 3549

Position of start ATG in wt / mu cDNA

91 / 91

Last intron/exon boundary

3477

Theoretical NMD boundary in CDS

3336

Length of CDS

3459

Coding sequence (CDS) position

230

cDNA position

320

gDNA position

5524

Chromosomal position

31265490

Speed

0.09 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:

16:31265490G>A_1_ENST00000648685

Back to summary table

Prediction:

BenignPermalink

Summary:

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

Model: simple_aae
Tree vote: 25|75 (del | benign) ?
Automatic classification due to gnomAD

Analysed issue

Analysis result

Variant

Chr16:31265490G>A (GRCh38)

Gene symbol

ITGAM

Gene constraints

LOEUF: 0.67, LOF (oe): 0.55, misssense (oe): 0.90, synonymous (oe): 0.98 ? (gnomAD)

Ensembl transcript ID

ENST00000648685.1

Genbank transcript ID

NM_001145808 (by similarity)

UniProt / AlphaMissense peptide

ITAM_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.230G>A
g.5524G>A

AA changes

AAE:	R77H	?
Score:	29

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

dbSNP ID	rs1143679
gnomAD	homozygous (A/A)	heterozygous	allele carriers
	8785	>32000	>32000

Protein conservation

Species	Match	AA	Alignment
Human		77	C	D	Y	S	T	G	S	C	E	P	I	R	L	Q	V	P	V	E	A	V	N	M	S	L
mutated	not conserved	77	C	D	Y	S	T	G	S	C	E	P	I	H	L	Q	V	P	V	E	A	V	N	M	S
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
17	1104	TOPO_DOM	Extracellular	lost
17	1152	CHAIN		lost
76	135	REPEAT	FG-GAP	lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	-0.236	0
	-1.519	0
(flanking)	-0.049	0.001

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

9

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

16

Strand

1

Original gDNA sequence snippet

AGGCTCATGCGAGCCCATCCGCCTGCAGGGTGAGTCACTGC

Altered gDNA sequence snippet

AGGCTCATGCGAGCCCATCCACCTGCAGGGTGAGTCACTGC

Original cDNA sequence snippet

AGGCTCATGCGAGCCCATCCGCCTGCAGGTCCCCGTGGAGG

Altered cDNA sequence snippet

AGGCTCATGCGAGCCCATCCACCTGCAGGTCCCCGTGGAGG

Wildtype AA sequence

MALRVLLLTA LTLCHGFNLD TENAMTFQEN ARGFGQSVVQ LQGSRVVVGA PQEIVAANQR
GSLYQCDYST GSCEPIRLQV PVEAVNMSLG LSLAATTSPP QLLACGPTVH QTCSENTYVK
GLCFLFGSNL RQQPQKFPEA LRGCPQEDSD IAFLIDGSGS IIPHDFRRMK EFVSTVMEQL
KKSKTLFSLM QYSEEFRIHF TFKEFQNNPN PRSLVKPITQ LLGRTHTATG IRKVVRELFN
ITNGARKNAF KILVVITDGE KFGDPLGYED VIPEADREGV IRYVIGVGDA FRSEKSRQEL
NTIASKPPRD HVFQVNNFEA LKTIQNQLRE KIFAIEGTQT GSSSSFEHEM SQEGFSAAIT
SNGPLLSTVG SYDWAGGVFL YTSKEKSTFI NMTRVDSDMN DAYLGYAAAI ILRNRVQSLV
LGAPRYQHIG LVAMFRQNTG MWESNANVKG TQIGAYFGAS LCSVDVDSNG STDLVLIGAP
HYYEQTRGGQ VSVCPLPRGQ RARWQCDAVL YGEQGQPWGR FGAALTVLGD VNGDKLTDVA
IGAPGEEDNR GAVYLFHGTS GSGISPSHSQ RIAGSKLSPR LQYFGQSLSG GQDLTMDGLV
DLTVGAQGHV LLLRSQPVLR VKAIMEFNPR EVARNVFECN DQVVKGKEAG EVRVCLHVQK
STRDRLREGQ IQSVVTYDLA LDSGRPHSRA VFNETKNSTR RQTQVLGLTQ TCETLKLQLP
NCIEDPVSPI VLRLNFSLVG TPLSAFGNLR PVLAEDAQRL FTALFPFEKN CGNDNICQDD
LSITFSFMSL DCLVVGGPRE FNVTVTVRND GEDSYRTQVT FFFPLDLSYR KVSTLQNQRS
QRSWRLACES ASSTEVSGAL KSTSCSINHP IFPENSEVTF NITFDVDSKA SLGNKLLLKA
NVTSENNMPR TNKTEFQLEL PVKYAVYMVV TSHGVSTKYL NFTASENTSR VMQHQYQVSN
LGQRSLPISL VFLVPVRLNQ TVIWDRPQVT FSENLSSTCH TKERLPSHSD FLAELRKAPV
VNCSIAVCQR IQCDIPFFGI QEEFNATLKG NLSFDWYIKT SHNHLLIVST AEILFNDSVF
TLLPGQGAFV RSQTETKVEP FEVPNPLPLI VGSSVGGLLL LALITAALYK LGFFKRQYKD
MMSEGGPPGA EPQ*

Mutated AA sequence

MALRVLLLTA LTLCHGFNLD TENAMTFQEN ARGFGQSVVQ LQGSRVVVGA PQEIVAANQR
GSLYQCDYST GSCEPIHLQV PVEAVNMSLG LSLAATTSPP QLLACGPTVH QTCSENTYVK
GLCFLFGSNL RQQPQKFPEA LRGCPQEDSD IAFLIDGSGS IIPHDFRRMK EFVSTVMEQL
KKSKTLFSLM QYSEEFRIHF TFKEFQNNPN PRSLVKPITQ LLGRTHTATG IRKVVRELFN
ITNGARKNAF KILVVITDGE KFGDPLGYED VIPEADREGV IRYVIGVGDA FRSEKSRQEL
NTIASKPPRD HVFQVNNFEA LKTIQNQLRE KIFAIEGTQT GSSSSFEHEM SQEGFSAAIT
SNGPLLSTVG SYDWAGGVFL YTSKEKSTFI NMTRVDSDMN DAYLGYAAAI ILRNRVQSLV
LGAPRYQHIG LVAMFRQNTG MWESNANVKG TQIGAYFGAS LCSVDVDSNG STDLVLIGAP
HYYEQTRGGQ VSVCPLPRGQ RARWQCDAVL YGEQGQPWGR FGAALTVLGD VNGDKLTDVA
IGAPGEEDNR GAVYLFHGTS GSGISPSHSQ RIAGSKLSPR LQYFGQSLSG GQDLTMDGLV
DLTVGAQGHV LLLRSQPVLR VKAIMEFNPR EVARNVFECN DQVVKGKEAG EVRVCLHVQK
STRDRLREGQ IQSVVTYDLA LDSGRPHSRA VFNETKNSTR RQTQVLGLTQ TCETLKLQLP
NCIEDPVSPI VLRLNFSLVG TPLSAFGNLR PVLAEDAQRL FTALFPFEKN CGNDNICQDD
LSITFSFMSL DCLVVGGPRE FNVTVTVRND GEDSYRTQVT FFFPLDLSYR KVSTLQNQRS
QRSWRLACES ASSTEVSGAL KSTSCSINHP IFPENSEVTF NITFDVDSKA SLGNKLLLKA
NVTSENNMPR TNKTEFQLEL PVKYAVYMVV TSHGVSTKYL NFTASENTSR VMQHQYQVSN
LGQRSLPISL VFLVPVRLNQ TVIWDRPQVT FSENLSSTCH TKERLPSHSD FLAELRKAPV
VNCSIAVCQR IQCDIPFFGI QEEFNATLKG NLSFDWYIKT SHNHLLIVST AEILFNDSVF
TLLPGQGAFV RSQTETKVEP FEVPNPLPLI VGSSVGGLLL LALITAALYK LGFFKRQYKD
MMSEGGPPGA EPQ*

Position of stopcodon in wt / mu CDS

3462 / 3462

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

1154 / 1154

Position of stopcodon in wt / mu cDNA

3560 / 3560

Position of start ATG in wt / mu cDNA

99 / 99

Last intron/exon boundary

3488

Theoretical NMD boundary in CDS

3339

Length of CDS

3462

Coding sequence (CDS) position

230

cDNA position

328

gDNA position

5524

Chromosomal position

31265490

Speed

0.11 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