NM_138425.4(C12orf57):c.33G>C (p.Leu11Phe) AND Temtamy syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 16, 2022
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:: RCV001316336.5

Allele description

NM_138425.4(C12orf57):c.33G>C (p.Leu11Phe)

Gene:

C12orf57:chromosome 12 open reading frame 57 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NM_138425.4(C12orf57):c.33G>C (p.Leu11Phe)

HGVS:

NC_000012.12:g.6944154G>C
NG_008047.1:g.24692G>C
NG_034262.1:g.5338G>C
NM_001301834.1:c.33G>C
NM_001301836.2:c.14-322G>C
NM_001301837.2:c.33G>C
NM_001301838.2:c.-169G>C
NM_138425.4:c.33G>CMANE SELECT
NP_001288763.1:p.Leu11Phe
NP_001288766.1:p.Leu11Phe
NP_612434.1:p.Leu11Phe
NC_000012.11:g.7053317G>C
NR_126035.2:n.133G>C

Protein change:

L11F

Links:

dbSNP: rs782168213

NCBI 1000 Genomes Browser:

rs782168213

Molecular consequence:

NM_001301838.2:c.-169G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001301836.2:c.14-322G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001301834.1:c.33G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001301837.2:c.33G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_138425.4:c.33G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_126035.2:n.133G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Temtamy syndrome (TEMTYS)
Synonyms:: Dysmorphism, corpus callosum agenesis and colobomas; Craniofacial dysmorphism with ocular coloboma absent corpus callosum and aortic dilatation; MENTAL RETARDATION WITH OR WITHOUT CRANIOFACIAL DYSMORPHISM, OCULAR COLOBOMA, OR ABNORMAL CORPUS CALLOSUM
Identifiers:: MONDO: MONDO:0009033; MedGen: C1857512; Orphanet: 1777; OMIM: 218340

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001506952	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 16, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 29269699, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001506952

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 16, 2022)

germline

clinical testing

PubMed (2)
[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

Next Generation Sequencing and Genome-Wide Genotyping Identify the Genetic Causes of Intellectual Disability in Ten Consanguineous Families from Jordan.

Froukh TJ.

Tohoku J Exp Med. 2017 Dec;243(4):297-309. doi: 10.1620/tjem.243.297.

PubMed [citation]

PMID:: 29269699

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 Invitae, SCV001506952.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 11 of the C12orf57 protein (p.Leu11Phe). This variant is present in population databases (rs782168213, gnomAD 0.008%). This missense change has been observed in individual(s) with clinical features of Temtamy syndrome (PMID: 29269699). ClinVar contains an entry for this variant (Variation ID: 1017217). 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: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Aug 25, 2024

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