X-100661933-GTTTTTTTTTTTTTTT-GTTTTTTTTTTTT

Variant names:

• chrX-100661933-GTTT-G
• rs771852530
• NM_014467.3:c.164-219_164-217delTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_014467.3(SRPX2):​c.164-219_164-217delTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000067 (0 hom., 0 hem., cov: 16)
• Consequence: SRPX2 NM_014467.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07

Genes affected

SRPX2 (HGNC:30668): (sushi repeat containing protein X-linked 2) This gene encodes a secreted protein that contains three sushi repeat motifs. The encoded protein may play a role in the development of speech and language centers in the brain. This protein may also be involved in angiogenesis. Mutations in this gene are the cause of bilateral perisylvian polymicrogyria, rolandic epilepsy, speech dyspraxia and cognitive disability. [provided by RefSeq, May 2010]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRPX2	NM_014467.3	c.164-219_164-217delTTT		intron_variant	Intron 3 of 10	ENST00000373004.5	NP_055282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRPX2	ENST00000373004.5	c.164-242_164-240delTTT		intron_variant	Intron 3 of 10	1	NM_014467.3	ENSP00000362095.3

Frequencies

GnomAD3 genomes AF: 0.0000670 AC: 4 AN: 59697 Hom.: 0 Cov.: 16

Gnomad AFR AF: 0.000142

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000615

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000670 AC: 4 AN: 59697 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 13233

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.000142 AC: 2 AN: 14087

American (AMR) AF: 0.00 AC: 0 AN: 5357

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 1672

East Asian (EAS) AF: 0.00 AC: 0 AN: 1875

South Asian (SAS) AF: 0.00 AC: 0 AN: 1163

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1650

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 115

European-Non Finnish (NFE) AF: 0.0000615 AC: 2 AN: 32521

Other (OTH) AF: 0.00 AC: 0 AN: 807

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.001946), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 27

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

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

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Other links and lift over

dbSNP: rs771852530; hg19: chrX-99916930;