NM_001174089.2(SLC4A11):c.425_432del (p.Arg142fs) AND Congenital hereditary endothelial dystrophy of cornea

Germline classification:: 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:: RCV004546409.1

Allele description [Variation Report for NM_001174089.2(SLC4A11):c.425_432del (p.Arg142fs)]

NM_001174089.2(SLC4A11):c.425_432del (p.Arg142fs)

Gene:

SLC4A11:solute carrier family 4 member 11 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_001174089.2(SLC4A11):c.425_432del (p.Arg142fs)

HGVS:

NC_000020.11:g.3234174GGCGAAGC[1]
NG_017072.1:g.10053GCTTCGCC[1]
NM_001174089.2:c.425_432delMANE SELECT
NM_001174090.2:c.554_561del
NM_001363745.2:c.425_432del
NM_032034.4:c.473_480del
NP_001167560.1:p.Arg142fs
NP_001167561.1:p.Arg185fs
NP_001350674.1:p.Arg142fs
NP_114423.1:p.Arg158fs
NC_000020.10:g.3214820GGCGAAGC[1]
NC_000020.10:g.3214820_3214827del
NM_001174089.2:c.425_432del
NM_032034.3:c.473_480del
NR_135000.1:n.585GCTTCGCC[1]

Protein change:

R142fs

Links:

OMIM: 610206.0009; dbSNP: rs869320721

NCBI 1000 Genomes Browser:

rs869320721

Molecular consequence:

NM_001174089.2:c.425_432del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001174090.2:c.554_561del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001363745.2:c.425_432del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_032034.4:c.473_480del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_135000.1:n.585GCTTCGCC[1] - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Congenital hereditary endothelial dystrophy of cornea
Synonyms:: Corneal dystrophy, congenital hereditary endothelial; Congenital hereditary endothelial dystrophy of the cornea; Maumenee corneal dystrophy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009019; MedGen: C1857569; Orphanet: 293603; OMIM: 217700

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005042706	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	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

SCV005042706

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

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 Neuberg Centre For Genomic Medicine, NCGM, SCV005042706.1

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

Description

The frameshift c.425_432del p.Arg142GlnfsTer4 variant in SLC4A11 gene has been previously reported in multiple individuals affected with corneal endothelial dystrophy Desir et al., 2007; Sultana et al., 2007. The p.Arg142GlnfsTer4 variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This variant has been reported to the ClinVar database as Pathogenic multiple submissions. The variant p.Arg142GlnfsTer4 causes a frameshift change starting with codon Arginine 142, changes this amino acid to Glutamine residue, and creates a premature Stop codon at position 4 of the new reading frame, denoted p.Arg142GlnfsTer4. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as 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: Sep 29, 2024

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