GeneBe

rs766593441

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_031291.4(SLC25A31):​c.715C>G​(p.Leu239Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L239F) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

SLC25A31
NM_031291.4 missense

Scores

1
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.292

Publications

0 publications found
Variant links:
Genes affected
SLC25A31 (HGNC:25319): (solute carrier family 25 member 31) The protein encoded by this gene is a member of the ADP/ATP carrier family of proteins that exchange cytosolic ADP for matrix ATP in the mitochondria. Cells over-expressing this gene have been shown to display an anti-apoptotic phenotype. This protein is also thought to play a role in spermatogenesis, where it is believed to associate with a part of the flagellar cytoskeleton and with glycolytic enzymes. Male mice with mutations in the mouse ortholog of this gene are sterile and spermatocytes display an early meiotic arrest phenotype. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2016]

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.051844597).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031291.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC25A31
NM_031291.4
MANE Select
c.715C>Gp.Leu239Val
missense
Exon 5 of 6NP_112581.1Q9H0C2
SLC25A31
NM_001318467.2
c.715C>Gp.Leu239Val
missense
Exon 5 of 7NP_001305396.1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
SLC25A31
ENST00000281154.6
TSL:1 MANE Select
c.715C>Gp.Leu239Val
missense
Exon 5 of 6ENSP00000281154.4Q9H0C2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00000405
AC:
1
AN:
246854
AF XY:
0.00000749
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000552
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.091
BayesDel_addAF
Benign
-0.31
T
BayesDel_noAF
Benign
-0.51
CADD
Benign
17
DANN
Benign
0.099
DEOGEN2
Benign
0.11
T
Eigen
Benign
-1.1
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.12
N
LIST_S2
Uncertain
0.94
D
M_CAP
Benign
0.0052
T
MetaRNN
Benign
0.052
T
MetaSVM
Benign
-0.98
T
MutationAssessor
Benign
-0.67
N
PhyloP100
-0.29
PrimateAI
Benign
0.45
T
PROVEAN
Benign
0.65
N
REVEL
Benign
0.15
Sift
Benign
0.85
T
Sift4G
Benign
0.91
T
Polyphen
0.0020
B
Vest4
0.12
MutPred
0.22
Gain of helix (P = 0.2059)
MVP
0.19
MPC
0.33
ClinPred
0.052
T
GERP RS
2.7
Varity_R
0.057
gMVP
0.37
Mutation Taster
=86/14
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs766593441; hg19: chr4-128689988; API