NM_017780.4(CHD7):c.3082A>G (p.Ile1028Val) AND not provided

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Mar 2, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000081828.21

Allele description [Variation Report for NM_017780.4(CHD7):c.3082A>G (p.Ile1028Val)]

NM_017780.4(CHD7):c.3082A>G (p.Ile1028Val)

Gene:

CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q12.2

Genomic location:

Preferred name:

NM_017780.4(CHD7):c.3082A>G (p.Ile1028Val)

HGVS:

NC_000008.11:g.60822627A>G
NG_007009.1:g.148848A>G
NM_001316690.1:c.1717-39602A>G
NM_017780.4:c.3082A>GMANE SELECT
NP_060250.2:p.Ile1028Val
NP_060250.2:p.Ile1028Val
NP_060250.2:p.Ile1028Val
LRG_176t1:c.3082A>G
LRG_176:g.148848A>G
LRG_176p1:p.Ile1028Val
NC_000008.10:g.61735186A>G
NM_017780.2:c.3082A>G
NM_017780.3:c.3082A>G
Q9P2D1:p.Ile1028Val

Protein change:

I1028V; ILE1028VAL

Links:

UniProtKB: Q9P2D1#VAR_021059; OMIM: 608892.0001; dbSNP: rs121434338

NCBI 1000 Genomes Browser:

rs121434338

Molecular consequence:

NM_001316690.1:c.1717-39602A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_017780.4:c.3082A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000329259	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Mar 2, 2023)	germline	clinical testing	Citation Link,
SCV000331477	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions)	Pathogenic (Aug 27, 2013)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000329259

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Pathogenic
(Mar 2, 2023)

germline

clinical testing

Citation Link,

SCV000331477

Eurofins Ntd Llc (ga)

criteria provided, single submitter

(EGL Classification Definitions)

Pathogenic
(Aug 27, 2013)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000329259.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Published functional studies demonstrate a damaging effect; the I1028V variant causes a complete loss of function of CHD7 (Balasubramanian et al., 2014); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20884005, 16155193, 18073582, 25472840, 15300250, 22539353, 26563674, 22461308, 28475860, 21158681, 32914532, 34828433, 33189935)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Eurofins Ntd Llc (ga), SCV000331477.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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