NM_004715.5(CTDP1):c.28C>T (p.Pro10Ser) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 13, 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:: RCV002025969.2

Allele description

NM_004715.5(CTDP1):c.28C>T (p.Pro10Ser)

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.28C>T (p.Pro10Ser)

HGVS:

NC_000018.10:g.79679975C>T
NG_007988.1:g.5175C>T
NM_001318511.2:c.28C>T
NM_004715.5:c.28C>TMANE SELECT
NM_048368.4:c.28C>T
NP_001305440.1:p.Pro10Ser
NP_004706.3:p.Pro10Ser
NP_430255.2:p.Pro10Ser
LRG_236:g.5175C>T
NC_000018.9:g.77439975C>T

Protein change:

P10S

Links:

dbSNP: rs1055392587

NCBI 1000 Genomes Browser:

rs1055392587

Molecular consequence:

NM_001318511.2:c.28C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004715.5:c.28C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_048368.4:c.28C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Gambusia affinis acetylserotonin O-methyltransferase 2 (asmt2), mRNA
PREDICTED: Gambusia affinis acetylserotonin O-methyltransferase 2 (asmt2), mRNA
gi|2106649952|ref|XM_044142926.1|

Nucleotide
Homo sapiens nucleoporin 205kDa, mRNA (cDNA clone IMAGE:4993878), partial cds
Homo sapiens nucleoporin 205kDa, mRNA (cDNA clone IMAGE:4993878), partial cds
gi|39645575|gb|BC063612.1|

Nucleotide
BF (13)
ClinVar
BF AND (alive[prop]) (845)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002294116	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 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

SCV002294116

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 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, SCV002294116.2

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

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 10 of the CTDP1 protein (p.Pro10Ser). This variant is present in population databases (no rsID available, gnomAD 0.05%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with CTDP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1504142). 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 serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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: Dec 24, 2023

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