NM_021964.3(ZNF148):c.1913C>A (p.Pro638Gln) AND not provided

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 19, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002040295.6

Allele description [Variation Report for NM_021964.3(ZNF148):c.1913C>A (p.Pro638Gln)]

NM_021964.3(ZNF148):c.1913C>A (p.Pro638Gln)

Genes:

LOC126806798:P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:124950809-124952008 [Gene]
ZNF148:zinc finger protein 148 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q21.2

Genomic location:

Preferred name:

NM_021964.3(ZNF148):c.1913C>A (p.Pro638Gln)

HGVS:

NC_000003.12:g.125232813G>T
NG_052987.1:g.147542C>A
NM_001348424.1:c.1913C>A
NM_001348425.2:c.1913C>A
NM_001348426.2:c.1913C>A
NM_001348427.2:c.1913C>A
NM_001348428.2:c.1913C>A
NM_001348429.2:c.1913C>A
NM_001348430.2:c.1913C>A
NM_001348431.2:c.1913C>A
NM_001348432.2:c.1913C>A
NM_001348433.2:c.1913C>A
NM_001348434.2:c.1787C>A
NM_021964.3:c.1913C>AMANE SELECT
NP_001335353.1:p.Pro638Gln
NP_001335354.1:p.Pro638Gln
NP_001335355.1:p.Pro638Gln
NP_001335356.1:p.Pro638Gln
NP_001335357.1:p.Pro638Gln
NP_001335358.1:p.Pro638Gln
NP_001335359.1:p.Pro638Gln
NP_001335360.1:p.Pro638Gln
NP_001335361.1:p.Pro638Gln
NP_001335362.1:p.Pro638Gln
NP_001335363.1:p.Pro596Gln
NP_068799.2:p.Pro638Gln
NC_000003.11:g.124951657G>T

Protein change:

P596Q

Links:

dbSNP: rs2107830116

NCBI 1000 Genomes Browser:

rs2107830116

Molecular consequence:

NM_001348424.1:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348425.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348426.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348427.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348428.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348429.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348430.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348431.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348432.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348433.2:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001348434.2:c.1787C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021964.3:c.1913C>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002300328	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Feb 19, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002300328

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Feb 19, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002300328.3

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

Description

This sequence change replaces proline with glutamine at codon 638 of the ZNF148 protein (p.Pro638Gln). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and glutamine. This variant is not present in population databases (ExAC no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has been observed in individual(s) with clinical features of intellectual disability syndrome (Invitae). In at least one individual the variant was observed to be de novo.

#	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		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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