8-56316157-C-T

Variant names:

• chr8-56316157-C-T
• rs376777147
• NM_138969.4:c.191G>A

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_138969.4(SDR16C5):​c.191G>A​(p.Gly64Glu) 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 pathogenic 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. G64A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SDR16C5 NM_138969.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.22

Genes affected

SDR16C5 (HGNC:30311): (short chain dehydrogenase/reductase family 16C member 5) This gene encodes a member of the short-chain alcohol dehydrogenase/reductase superfamily of proteins and is involved in the oxidation of retinol to retinaldehyde. The encoded protein is associated with the endoplasmic reticulum and is predicted to contain three transmembrane helices, suggesting that it is an integral membrane protein. It recognizes all-trans-retinol and all-trans-retinaldehyde as substrates and exhibits a strong preference for NAD(+)/NADH as cofactors. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.898

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SDR16C5	NM_138969.4	c.191G>A	p.Gly64Glu	missense_variant	Exon 2 of 7	ENST00000303749.8	NP_620419.2
SDR16C5	NM_001318049.2	c.191G>A	p.Gly64Glu	missense_variant	Exon 2 of 8		NP_001304978.1
SDR16C5	NM_001318050.2	c.191G>A	p.Gly64Glu	missense_variant	Exon 2 of 6		NP_001304979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SDR16C5	ENST00000303749.8	c.191G>A	p.Gly64Glu	missense_variant	Exon 2 of 7	1	NM_138969.4	ENSP00000307607.3
SDR16C5	ENST00000396721.6	c.191G>A	p.Gly64Glu	missense_variant	Exon 2 of 6	1		ENSP00000379947.2
SDR16C5	ENST00000522671.1	c.191G>A	p.Gly64Glu	missense_variant	Exon 2 of 8	2		ENSP00000431010.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.42
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.17
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.81	.;D;D
Eigen	Uncertain	0.44
Eigen_PC	Uncertain	0.29
FATHMM_MKL	Uncertain	0.79	D
LIST_S2	Uncertain	0.87	D;T;T
M_CAP	Uncertain	0.24	D
MetaRNN	Pathogenic	0.90	D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.2	M;M;.
PrimateAI	Benign	0.44	T
PROVEAN	Pathogenic	-4.7	D;D;D
REVEL	Pathogenic	0.65
Sift	Benign	0.066	T;T;D
Sift4G	Uncertain	0.058	T;T;T
Polyphen		1.0	D;P;D
Vest4		0.72
MutPred		0.74		Gain of solvent accessibility (P = 0.0145);Gain of solvent accessibility (P = 0.0145);Gain of solvent accessibility (P = 0.0145);
MVP		0.94
MPC		0.32
ClinPred		1.0	D
GERP RS		5.1
Varity_R		0.46
gMVP		0.85

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

LitVar

Other links and lift over

dbSNP: rs376777147; hg19: chr8-57228716; COSMIC: COSV58125175;