NM_004715.5(CTDP1):c.46A>C (p.Thr16Pro) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 4, 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:: RCV003037578.2

Allele description

NM_004715.5(CTDP1):c.46A>C (p.Thr16Pro)

Gene:

CTDP1:CTD phosphatase subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q23

Genomic location:

Preferred name:

NM_004715.5(CTDP1):c.46A>C (p.Thr16Pro)

HGVS:

NC_000018.10:g.79679993A>C
NG_007988.1:g.5193A>C
NG_139250.1:g.658A>C
NM_001318511.2:c.46A>C
NM_004715.5:c.46A>CMANE SELECT
NM_048368.4:c.46A>C
NP_001305440.1:p.Thr16Pro
NP_004706.3:p.Thr16Pro
NP_004706.3:p.Thr16Pro
NP_430255.2:p.Thr16Pro
LRG_236t1:c.46A>C
LRG_236:g.5193A>C
LRG_236p1:p.Thr16Pro
NC_000018.9:g.77439993A>C
NM_004715.4:c.46A>C

Protein change:

T16P

Molecular consequence:

NM_001318511.2:c.46A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_004715.5:c.46A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_048368.4:c.46A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood...
Homo sapiens globoside alpha-1,3-N-acetylgalactosaminyltransferase 1 (FORS blood group) (GBGT1), transcript variant 2, mRNA
gi|544063401|ref|NM_001282629.1|

Nucleotide
Mus musculus CUGBP, Elav-like family member 4 (Celf4), transcript variant 22, mR...
Mus musculus CUGBP, Elav-like family member 4 (Celf4), transcript variant 22, mRNA
gi|1376476228|ref|NM_001362291.1|

Nucleotide
Mus musculus CUGBP, Elav-like family member 4 (Celf4), transcript variant 49, mR...
Mus musculus CUGBP, Elav-like family member 4 (Celf4), transcript variant 49, mRNA
gi|1376477004|ref|NM_001362329.1|

Nucleotide
Mus musculus CUGBP, Elav-like family member 4 (Celf4), transcript variant 53, mR...
Mus musculus CUGBP, Elav-like family member 4 (Celf4), transcript variant 53, mRNA
gi|1376476234|ref|NM_001362334.1|

Nucleotide
CUGBP Elav-like family member 4 isoform X7 [Mus musculus]
CUGBP Elav-like family member 4 isoform X7 [Mus musculus]
gi|569003005|ref|XP_006525581.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003322784	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 4, 2022)	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

SCV003322784

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 4, 2022)

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV003322784.2

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The proline amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with CTDP1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces threonine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 16 of the CTDP1 protein (p.Thr16Pro). 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

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