NM_138425.4(C12orf57):c.136_138del (p.Asp46del) AND Temtamy syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 27, 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:: RCV000543431.7

Allele description [Variation Report for NM_138425.4(C12orf57):c.136_138del (p.Asp46del)]

NM_138425.4(C12orf57):c.136_138del (p.Asp46del)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

12p13.31

Genomic location:

Preferred name:

NM_138425.4(C12orf57):c.136_138del (p.Asp46del)

HGVS:

NC_000012.12:g.6944559_6944561del
NG_034262.1:g.5743_5745del
NM_001301834.1:c.136_138del
NM_001301836.2:c.97_99del
NM_001301837.2:c.136_138del
NM_001301838.2:c.31_33del
NM_138425.4:c.136_138delMANE SELECT
NP_001288763.1:p.Asp46del
NP_001288765.1:p.Asp33del
NP_001288766.1:p.Asp46del
NP_001288767.1:p.Asp11del
NP_612434.1:p.Asp46del
NC_000012.11:g.7053720_7053722del
NC_000012.11:g.7053722_7053724del
NM_138425.2:c.136_138del
NM_138425.3:c.136_138del
NM_138425.3:c.136_138delGAC
NR_126035.2:n.332_334del

Protein change:

D11del

Links:

dbSNP: rs781925545

NCBI 1000 Genomes Browser:

rs781925545

Molecular consequence:

NM_001301834.1:c.136_138del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001301836.2:c.97_99del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001301837.2:c.136_138del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001301838.2:c.31_33del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_138425.4:c.136_138del - inframe_deletion - [Sequence Ontology: SO:0001822]
NR_126035.2:n.332_334del - 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
SCV000641930	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 27, 2023)	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

SCV000641930

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 27, 2023)

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000641930.6

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

Description

This variant, c.136_138del, results in the deletion of 1 amino acid(s) of the C12orf57 protein (p.Asp46del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs781925545, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with C12orf57-related conditions. ClinVar contains an entry for this variant (Variation ID: 210546). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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: Feb 20, 2024

ClinVar

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