rs104894915

Positions:

• chrX-154187939-C-A

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PP3_Strong PP5

The NM_000513.2(OPN1MW):​c.282C>A​(p.Asn94Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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: 2)
• Consequence: OPN1MW NM_000513.2 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 1.92

Genes affected

OPN1MW (HGNC:4206): (opsin 1, medium wave sensitive) This gene encodes for a light absorbing visual pigment of the opsin gene family. The encoded protein is called green cone photopigment or medium-wavelength sensitive opsin. Opsins are G-protein coupled receptors with seven transmembrane domains, an N-terminal extracellular domain, and a C-terminal cytoplasmic domain. The long-wavelength opsin gene and multiple copies of the medium-wavelength opsin gene are tandemly arrayed on the X chromosome and frequent unequal recombination and gene conversion may occur between these sequences. X chromosomes may have fusions of the medium- and long-wavelength opsin genes or may have more than one copy of these genes. Defects in this gene are the cause of deutanopic colorblindness. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 5 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.97
• PP5: Variant X-154187939-C-A is Pathogenic according to our data. Variant chrX-154187939-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 10512.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OPN1MW	NM_000513.2	c.282C>A	p.Asn94Lys	missense_variant	2/6	ENST00000595290.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OPN1MW	ENST00000595290.6	c.282C>A	p.Asn94Lys	missense_variant	2/6	1	NM_000513.2	P1
OPN1MW	ENST00000595330.1	n.292C>A		non_coding_transcript_exon_variant	2/4	5

Frequencies

GnomAD3 genomes Cov.: 2

GnomAD4 exome Cov.: 8

GnomAD4 genome Cov.: 2

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Deuteranomaly Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jun 07, 2002

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.18	T
BayesDel_noAF	Benign	-0.50
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.60	D
FATHMM_MKL	Uncertain	0.85	D
M_CAP	Benign	0.017	T
MetaRNN	Pathogenic	0.97	D
MetaSVM	Benign	-0.56	T
MutationTaster	Benign	1.0	A
PrimateAI	Pathogenic	0.84	D
Sift4G	Pathogenic	0.0	D
Polyphen		0.0050	B
Vest4		0.97
MutPred		0.91		Gain of methylation at N94 (P = 0.0275);
MVP		0.95
ClinPred		0.99	D
GERP RS		2.9
Varity_R		0.93
gMVP		0.98

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: rs104894915; hg19: chrX-153453428;