NM_003410.4:c.115_116delGT

Variant names:

• chrX-24179237-CTG-C
• NM_003410.4:c.115_116delGT

Variant summary

Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_003410.4(ZFX):​c.115_116delGT​(p.Val39PhefsTer14) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 23)
• Consequence: ZFX NM_003410.4 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 7.68
• Publications: 0 publications found

Genes affected

ZFX (HGNC:12869): (zinc finger protein X-linked) This gene on the X chromosome is structurally similar to a related gene on the Y chromosome. It encodes a member of the krueppel C2H2-type zinc-finger protein family. The full-length protein contains an acidic transcriptional activation domain (AD), a nuclear localization sequence (NLS) and a DNA binding domain (DBD) consisting of 13 C2H2-type zinc fingers. Studies in mouse embryonic and adult hematopoietic stem cells showed that this gene was required as a transcriptional regulator for self-renewal of both stem cell types, but it was dispensable for growth and differentiation of their progeny. Multiple alternatively spliced transcript variants encoding different isoforms have been identified, but the full-length nature of some variants has not been determined. [provided by RefSeq, May 2010]

ZFX Gene-Disease associations (from GenCC):

• intellectual developmental disorder, X-linked, syndromic 37

  Inheritance: XL Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-24179237-CTG-C is Pathogenic according to our data. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-24179237-CTG-C is described in CliVar as Pathogenic. Clinvar id is 3066053.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZFX	NM_003410.4	c.115_116delGT	p.Val39PhefsTer14	frameshift_variant	Exon 5 of 10	ENST00000304543.10	NP_003401.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZFX	ENST00000304543.10	c.115_116delGT	p.Val39PhefsTer14	frameshift_variant	Exon 5 of 10	5	NM_003410.4	ENSP00000304985.5

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: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Intellectual developmental disorder, X-linked, syndromic 37 Pathogenic:1

Apr 02, 2024

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.7

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

Other links and lift over

hg19: chrX-24197354; COSMIC: COSV100458204; COSMIC: COSV100458204;