NM_001174089.2(SLC4A11):c.2140C>T (p.Arg714Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 4, 2023
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:: RCV001235975.7

Allele description [Variation Report for NM_001174089.2(SLC4A11):c.2140C>T (p.Arg714Ter)]

NM_001174089.2(SLC4A11):c.2140C>T (p.Arg714Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_001174089.2(SLC4A11):c.2140C>T (p.Arg714Ter)

HGVS:

NC_000020.11:g.3228890G>A
NG_012093.2:g.25024G>A
NG_017072.1:g.15352C>T
NM_001174089.2:c.2140C>TMANE SELECT
NM_001174090.2:c.2269C>T
NM_001363745.2:c.2026C>T
NM_032034.4:c.2188C>T
NP_001167560.1:p.Arg714Ter
NP_001167561.1:p.Arg757Ter
NP_001350674.1:p.Arg676Ter
NP_114423.1:p.Arg730Ter
NC_000020.10:g.3209536G>A
NM_032034.3:c.2188C>T
NR_135000.1:n.2238C>T

Protein change:

R676*

Links:

dbSNP: rs772409032

NCBI 1000 Genomes Browser:

rs772409032

Molecular consequence:

NR_135000.1:n.2238C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001174089.2:c.2140C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001174090.2:c.2269C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363745.2:c.2026C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_032034.4:c.2188C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001408685	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 4, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 17220209, 17679935, 19369245, 25500497, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001408685

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 4, 2023)

germline

clinical testing

PubMed (5)
[See all records that cite these PMIDs]

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

Borate transporter SLC4A11 mutations cause both Harboyan syndrome and non-syndromic corneal endothelial dystrophy.

Desir J, Moya G, Reish O, Van Regemorter N, Deconinck H, David KL, Meire FM, Abramowicz MJ.

J Med Genet. 2007 May;44(5):322-6. Epub 2007 Jan 12.

PubMed [citation]

PMID:: 17220209
PMCID:: PMC2597979

Mutational spectrum of the SLC4A11 gene in autosomal recessive congenital hereditary endothelial dystrophy.

Sultana A, Garg P, Ramamurthy B, Vemuganti GK, Kannabiran C.

Mol Vis. 2007 Jul 26;13:1327-32.

PubMed [citation]

PMID:: 17679935

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001408685.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Arg730*) in the SLC4A11 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SLC4A11 are known to be pathogenic (PMID: 17220209, 17679935). This variant is present in population databases (rs772409032, gnomAD 0.0009%). This premature translational stop signal has been observed in individuals with congenital hereditary endothelial dystrophy (PMID: 19369245, 25500497). This variant is also known as Arg757*. ClinVar contains an entry for this variant (Variation ID: 962167). 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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 19, 2024

ClinVar

Relating variation to medicine