rs752023385

Variant names:

• chr1-109161931-C-G
• rs752023385
• NM_020775.5:c.191C>G

Your query was ambiguous. Multiple possible variants found:

• chr1-109161931-C-G
• chr1-109161931-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_020775.5(ELAPOR1):​c.191C>G​(p.Thr64Arg) 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. 13/21 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. T64A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 34)
• Consequence: ELAPOR1 NM_020775.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

Genes affected

ELAPOR1 (HGNC:29618): (endosome-lysosome associated apoptosis and autophagy regulator 1) Expression of this gene is induced by estrogen and the encoded protein has been characterized as a transmembrane protein. The encoded protein has been found in to correlate with survival in certain carcinomas (PMID: 21102415) and may be important for cellular response to stress (PMID: 21072319). Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.09789616).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELAPOR1	NM_020775.5	c.191C>G	p.Thr64Arg	missense_variant	Exon 2 of 22	ENST00000369939.8	NP_065826.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELAPOR1	ENST00000369939.8	c.191C>G	p.Thr64Arg	missense_variant	Exon 2 of 22	5	NM_020775.5	ENSP00000358955.3

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.078
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.45
CADD	Benign	16
DANN	Benign	0.97
DEOGEN2	Benign	0.062	T;T;.;.;T;T;.
Eigen	Benign	-0.53
Eigen_PC	Benign	-0.50
FATHMM_MKL	Benign	0.12	N
LIST_S2	Benign	0.74	T;T;T;T;T;T;T
M_CAP	Benign	0.010	T
MetaRNN	Benign	0.098	T;T;T;T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.3	.;.;.;.;L;.;L
PrimateAI	Uncertain	0.50	T
PROVEAN	Uncertain	-3.2	D;D;N;N;N;N;N
REVEL	Benign	0.085
Sift	Uncertain	0.023	D;T;T;T;T;T;T
Sift4G	Benign	0.074	T;T;T;T;T;T;T
Polyphen		0.45, 0.69	.;.;.;.;B;.;P
Vest4		0.30, 0.27
MutPred		0.33		Gain of phosphorylation at S66 (P = 0.0658);Gain of phosphorylation at S66 (P = 0.0658);Gain of phosphorylation at S66 (P = 0.0658);Gain of phosphorylation at S66 (P = 0.0658);Gain of phosphorylation at S66 (P = 0.0658);Gain of phosphorylation at S66 (P = 0.0658);Gain of phosphorylation at S66 (P = 0.0658);
MVP		0.24
MPC		0.32
ClinPred		0.50	D
GERP RS		1.1
Varity_R		0.11
gMVP		0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.14		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: rs752023385; hg19: chr1-109704553;