rs587778765

chrX-15823096-CG-AT

Variant summary

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

The NM_005089.4(ZRSR2):c.1303_1304delinsAT(p.Arg435Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as not provided (no stars).

• Frequency: Genomes: not found (cov: 23)
• Consequence: ZRSR2 NM_005089.4 missense
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 1.18

Genes affected

ZRSR2 (HGNC:23019): (zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2) This gene encodes an essential splicing factor. The encoded protein associates with the U2 auxiliary factor heterodimer, which is required for the recognition of a functional 3' splice site in pre-mRNA splicing, and may play a role in network interactions during spliceosome assembly. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ZRSR2	NM_005089.4	c.1303_1304delinsAT	p.Arg435Met	missense_variant	11/11	ENST00000307771.8
ZRSR2	XM_011545589.4	c.1372_1373delinsAT	p.Arg458Met	missense_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ZRSR2	ENST00000307771.8	c.1303_1304delinsAT	p.Arg435Met	missense_variant	11/11	1	NM_005089.4	P2
ZRSR2	ENST00000684799.1	c.1225_1226delinsAT	p.Arg409Met	missense_variant	10/11			A2
ZRSR2	ENST00000690252.1	c.1303_1304delinsAT	p.Arg435Met	missense_variant, NMD_transcript_variant	11/13
ZRSR2	ENST00000691502.1	c.1189_1190delinsAT	p.Arg397Met	missense_variant, NMD_transcript_variant	11/13

Frequencies

GnomAD3 genomes Cov.: 23

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 23

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not specified Other:1

not provided, no classification provided

reference population

ITMI

Sep 19, 2013

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs587778765; hg19: chrX-15841219;