NM_031407.7(HUWE1):c.344C>T (p.Ser115Phe) AND X-linked intellectual disability

Germline classification:: Likely pathogenic (1 submission)
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:: RCV003335315.1

Allele description [Variation Report for NM_031407.7(HUWE1):c.344C>T (p.Ser115Phe)]

NM_031407.7(HUWE1):c.344C>T (p.Ser115Phe)

Gene:

HUWE1:HECT, UBA and WWE domain containing E3 ubiquitin protein ligase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp11.22

Genomic location:

Preferred name:

NM_031407.7(HUWE1):c.344C>T (p.Ser115Phe)

HGVS:

NC_000023.11:g.53647375G>A
NG_016261.2:g.44359C>T
NM_031407.7:c.344C>TMANE SELECT
NP_113584.3:p.Ser115Phe
NC_000023.10:g.53674318G>A
NM_031407.6:c.344C>T
p.(Ser115Phe)

Protein change:

S115F

Links:

dbSNP: rs1557036757

NCBI 1000 Genomes Browser:

rs1557036757

Molecular consequence:

NM_031407.7:c.344C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: X-linked intellectual disability (XLID)
Synonyms:: Mental retardation, X-linked; INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED
Identifiers:: MONDO: MONDO:0100284; MedGen: C1136249

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004046075	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	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

SCV004046075

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego, SCV004046075.1

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

Description

This variant has been previously reported as a de novo change in a female patient with X-linked intellectual disability (PMID: 29180823). That reported patient had abnormal X-inactivation studies (PMID: 29180823). It is absent from the gnomAD population database and thus is presumed to be rare. The c.344C>T (p.Ser115Phe) variant is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.344C>T (p.Ser115Phe) variant is classified as Likely Pathogenic.

#	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

Last Updated: May 7, 2024

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