rs587777670

Positions:

• chr6-53270660-C-A
• chr6-53270660-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2 PP3_Moderate PP5

The ENST00000304434.11(ELOVL5):​c.689G>T​(p.Gly230Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: ELOVL5 ENST00000304434.11 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1 O:1
• Conservation: PhyloP100: 7.90

Genes affected

ELOVL5 (HGNC:21308): (ELOVL fatty acid elongase 5) This gene belongs to the ELO family. It is highly expressed in the adrenal gland and testis, and encodes a multi-pass membrane protein that is localized in the endoplasmic reticulum. This protein is involved in the elongation of long-chain polyunsaturated fatty acids. Mutations in this gene have been associated with spinocerebellar ataxia-38 (SCA38). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.911
• PP5: Variant 6-53270660-C-A is Pathogenic according to our data. Variant chr6-53270660-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 144075.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chr6-53270660-C-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELOVL5	NM_021814.5	c.689G>T	p.Gly230Val	missense_variant	7/8	ENST00000304434.11	NP_068586.1
ELOVL5	NM_001242828.2	c.770G>T	p.Gly257Val	missense_variant	8/9		NP_001229757.1
ELOVL5	NM_001301856.2	c.689G>T	p.Gly230Val	missense_variant	7/8		NP_001288785.1
ELOVL5	NM_001242830.2	c.564G>T	p.Trp188Cys	missense_variant	6/7		NP_001229759.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELOVL5	ENST00000304434.11	c.689G>T	p.Gly230Val	missense_variant	7/8	1	NM_021814.5	ENSP00000306640	P1
ELOVL5	ENST00000542638.5	c.564G>T	p.Trp188Cys	missense_variant	6/7	1		ENSP00000440728
ELOVL5	ENST00000370918.8	c.770G>T	p.Gly257Val	missense_variant	8/9	2		ENSP00000359956

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Spinocerebellar ataxia type 38 Pathogenic:1 Other:1

not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 07, 2014	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.39
BayesDel_addAF	Pathogenic	0.23	D
BayesDel_noAF	Uncertain	0.090
CADD	Pathogenic	32
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.45	.;T
Eigen	Uncertain	0.53
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.95	D;D
M_CAP	Pathogenic	0.88	D
MetaRNN	Pathogenic	0.91	D;D
MetaSVM	Benign	-1.2	T
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Uncertain	0.70	T
PROVEAN	Uncertain	-4.1	.;D
REVEL	Pathogenic	0.76
Sift	Benign	0.051	.;T
Sift4G	Benign	0.082	T;T
Polyphen		0.98	.;D
Vest4		0.92
MutPred		0.64		.;Loss of helix (P = 0.2271);
MVP		0.52
ClinPred		0.98	D
GERP RS		5.9
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.61
gMVP		0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.38		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.38		Position offset: -17

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

Publications

LitVar

Other links and lift over

dbSNP: rs587777670; hg19: chr6-53135458;