MutationT@ster 2025

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Input seems to be ok - now mapping the variant to the different transcripts...
Querying Taster for transcript #1: ENST00000394077
Querying Taster for transcript #2: ENST00000495401
Querying Taster for transcript #3: ENST00000469605
MT speed 0.17 s - this script 2.580977 s

Transcript summary:

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Transcript	Gene symbol	Prediction	Tree vote	Model	Splice site change	Variant type	Protein length	Features at a glance
ENST00000394077(MANE Select)	RPL24	Deleterious	95\|5	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed Protein features (might be) affected
ENST00000469605	RPL24	Deleterious	97\|3	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed
ENST00000495401	RPL24	Deleterious	99\|1	simple_aae	No	Single base exchange	Normal	Amino acid sequence changed

MutationT@ster 2025

Variant:

3:101682795T>C_1_ENST00000394077

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Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed
Protein features (might be) affected

Model: simple_aae
Tree vote: 95|5 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:101682795T>C (GRCh38)

Gene symbol

RPL24

Gene constraints

LOEUF: 0.58, LOF (oe): 0.28, misssense (oe): 0.50, synonymous (oe): 1.07 ? (gnomAD)

Ensembl transcript ID

ENST00000394077.8

Genbank transcript ID

NM_000986 (exact from MANE)

UniProt / AlphaMissense peptide

RL24_HUMAN | AlphaMissense: transcript, gene

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.305A>G
g.3939A>G

AA changes

AAE:	K102R	?
Score:	26

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K	E
mutated	all conserved	102	M	A	K	R	N	Q	K	P	E	V	R	R	A	Q	R	E	Q	A	I	R	A	A	K
Ptroglodytes	all identical	102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K
Mmulatta	all identical	102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	K	Q	A	I	R	A	A	K
Fcatus	all identical	102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K
Mmusculus	all identical	102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K
Ggallus	all identical	140	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K
Trubripes	all identical	168	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K
Drerio	no homologue
Dmelanogaster	all identical	102	L	A	K	R	N	M	K	P	E	V	R	K	A	Q	R	D	Q	A	I	K	V	A	K
Celegans	all conserved	102	L	A	K	R	N	Q	T	E	D	F	R	R	Q	Q	R	E	Q	A	A	K	I	A	K
Xtropicalis	all identical	140	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K

Protein features

Start (aa)	End (aa)	Feature	Details
1	157	CHAIN		lost

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.751	1
	7.955	1
(flanking)	7.955	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

25

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

-1

Original gDNA sequence snippet

TCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTA

Altered gDNA sequence snippet

TCAGAAACCTGAAGTTAGAAGGGCTCAACGAGAACAAGCTA

Original cDNA sequence snippet

TCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTA

Altered cDNA sequence snippet

TCAGAAACCTGAAGTTAGAAGGGCTCAACGAGAACAAGCTA

Wildtype AA sequence

MKVELCSFSG YKIYPGHGRR YARTDGKVFQ FLNAKCESAF LSKRNPRQIN WTVLYRRKHK
KGQSEEIQKK RTRRAVKFQR AITGASLADI MAKRNQKPEV RKAQREQAIR AAKEAKKAKQ
ASKKTAMAAA KAPTKAAPKQ KIVKPVKVSA PRVGGKR*

Mutated AA sequence

MKVELCSFSG YKIYPGHGRR YARTDGKVFQ FLNAKCESAF LSKRNPRQIN WTVLYRRKHK
KGQSEEIQKK RTRRAVKFQR AITGASLADI MAKRNQKPEV RRAQREQAIR AAKEAKKAKQ
ASKKTAMAAA KAPTKAAPKQ KIVKPVKVSA PRVGGKR*

Position of stopcodon in wt / mu CDS

474 / 474

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

158 / 158

Position of stopcodon in wt / mu cDNA

516 / 516

Position of start ATG in wt / mu cDNA

43 / 43

Last intron/exon boundary

435

Theoretical NMD boundary in CDS

342

Length of CDS

474

Coding sequence (CDS) position

305

cDNA position

347

gDNA position

3939

Chromosomal position

101682795

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:

3:101682795T>C_3_ENST00000469605

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 97|3 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:101682795T>C (GRCh38)

Gene symbol

RPL24

Gene constraints

LOEUF: 0.67, LOF (oe): 0.32, misssense (oe): 0.50, synonymous (oe): 1.11 ? (gnomAD)

Ensembl transcript ID

ENST00000469605.2

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.305A>G
g.3939A>G

AA changes

AAE:	K102R	?
Score:	26

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	A	A	K	E
mutated	all conserved	102	M	A	K	R	N	Q	K	P	E	V	R	R	A	Q	R	E	Q	A	I	R	A	A	K
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.751	1
	7.955	1
(flanking)	7.955	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

25

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

-1

Original gDNA sequence snippet

TCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTA

Altered gDNA sequence snippet

TCAGAAACCTGAAGTTAGAAGGGCTCAACGAGAACAAGCTA

Original cDNA sequence snippet

TCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTA

Altered cDNA sequence snippet

TCAGAAACCTGAAGTTAGAAGGGCTCAACGAGAACAAGCTA

Wildtype AA sequence

MKVELCSFSG YKIYPGHGRR YARTDGKVFQ FLNAKCESAF LSKRNPRQIN WTVLYRRKHK
KGQSEEIQKK RTRRAVKFQR AITGASLADI MAKRNQKPEV RKAQREQAIR AAKEAKKAKQ
ASKKTAMAAA KVIMGFLYFL EQYNRKIFFF *

Mutated AA sequence

MKVELCSFSG YKIYPGHGRR YARTDGKVFQ FLNAKCESAF LSKRNPRQIN WTVLYRRKHK
KGQSEEIQKK RTRRAVKFQR AITGASLADI MAKRNQKPEV RRAQREQAIR AAKEAKKAKQ
ASKKTAMAAA KVIMGFLYFL EQYNRKIFFF *

Position of stopcodon in wt / mu CDS

453 / 453

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

151 / 151

Position of stopcodon in wt / mu cDNA

491 / 491

Position of start ATG in wt / mu cDNA

39 / 39

Last intron/exon boundary

367

Theoretical NMD boundary in CDS

278

Length of CDS

453

Coding sequence (CDS) position

305

cDNA position

343

gDNA position

3939

Chromosomal position

101682795

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:

3:101682795T>C_2_ENST00000495401

Back to summary table

Prediction:

DeleteriousPermalink

Summary:

Amino acid sequence changed

Model: simple_aae
Tree vote: 99|1 (del | benign) ?

Analysed issue

Analysis result

Variant

Chr3:101682795T>C (GRCh38)

Gene symbol

RPL24

Gene constraints

LOEUF: 0.88, LOF (oe): 0.47, misssense (oe): 0.51, synonymous (oe): 1.05 ? (gnomAD)

Ensembl transcript ID

ENST00000495401.5

Genbank transcript ID

UniProt / AlphaMissense peptide

N/A

Variant type

Single base exchange

Gene region

CDS

DNA changes

c.305A>G
g.3939A>G

AA changes

AAE:	K102R	?
Score:	26

Frameshift

No

Length of protein

Normal

Pathogenic variant (ClinVar)

Variant not listed in ClinVar as (likely) pathogenic.

Variant DBs

	Not in dbSNP
	Allele 'C' was not found in gnomAD

Protein conservation

Species	Match	AA	Alignment
Human		102	M	A	K	R	N	Q	K	P	E	V	R	K	A	Q	R	E	Q	A	I	R	H	L	Q	R
mutated	all conserved	102	M	A	K	R	N	Q	K	P	E	V	R	R	A	Q	R	E	Q	A	I	R	H	L	Q
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

N/A

Phylogenetic conservation

	PhyloP	PhastCons
(flanking)	1.751	1
	7.955	1
(flanking)	7.955	1

?

Splice sites

No abrogation of potential splice sites predicted by MaxEntScan.

Distance from splice site

25

Kozak consensus sequence altered?

No

poly(A) signal

N/A

AA sequence altered

Yes

Chromosome

3

Strand

-1

Original gDNA sequence snippet

TCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTA

Altered gDNA sequence snippet

TCAGAAACCTGAAGTTAGAAGGGCTCAACGAGAACAAGCTA

Original cDNA sequence snippet

TCAGAAACCTGAAGTTAGAAAGGCTCAACGAGAACAAGCTA

Altered cDNA sequence snippet

TCAGAAACCTGAAGTTAGAAGGGCTCAACGAGAACAAGCTA

Wildtype AA sequence

MKVELCSFSG YKIYPGHGRR YARTDGKVFQ FLNAKCESAF LSKRNPRQIN WTVLYRRKHK
KGQSEEIQKK RTRRAVKFQR AITGASLADI MAKRNQKPEV RKAQREQAIR HLQRQHLSKR
L*

Mutated AA sequence

MKVELCSFSG YKIYPGHGRR YARTDGKVFQ FLNAKCESAF LSKRNPRQIN WTVLYRRKHK
KGQSEEIQKK RTRRAVKFQR AITGASLADI MAKRNQKPEV RRAQREQAIR HLQRQHLSKR
L*

Position of stopcodon in wt / mu CDS

366 / 366

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

122 / 122

Position of stopcodon in wt / mu cDNA

395 / 395

Position of start ATG in wt / mu cDNA

30 / 30

Last intron/exon boundary

358

Theoretical NMD boundary in CDS

278

Length of CDS

366

Coding sequence (CDS) position

305

cDNA position

334

gDNA position

3939

Chromosomal position

101682795

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