NM_015426.5(POC1A):c.1085C>T (p.Thr362Met) AND Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome

Germline classification:: Uncertain significance (1 submission)
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:: RCV003339900.3

Allele description [Variation Report for NM_015426.5(POC1A):c.1085C>T (p.Thr362Met)]

NM_015426.5(POC1A):c.1085C>T (p.Thr362Met)

Gene:

POC1A:POC1 centriolar protein A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p21.2

Genomic location:

Preferred name:

NM_015426.5(POC1A):c.1085C>T (p.Thr362Met)

HGVS:

NC_000003.12:g.52096609G>A
NG_032947.1:g.63082C>T
NM_001161580.2:c.982-20624C>T
NM_001161581.2:c.971C>T
NM_015426.5:c.1085C>TMANE SELECT
NP_001155053.1:p.Thr324Met
NP_056241.3:p.Thr362Met
NC_000003.11:g.52130625G>A

Protein change:

T324M

Links:

dbSNP: rs186299883

NCBI 1000 Genomes Browser:

rs186299883

Molecular consequence:

NM_001161580.2:c.982-20624C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001161581.2:c.971C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015426.5:c.1085C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome
Synonyms:: SOFT SYNDROME; Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis
Identifiers:: MONDO: MONDO:0013894; MedGen: C3542022; Orphanet: 314394; OMIM: 614813

Recent activity

Clear Turn Off Turn On

exocyst complex component 3-like protein 2 [Homo sapiens]
exocyst complex component 3-like protein 2 [Homo sapiens]
gi|1838336134|ref|NP_001369351.1|

Protein
Companilactobacillus keshanensis strain 33-7, whole genome shotgun sequencing pr...
Companilactobacillus keshanensis strain 33-7, whole genome shotgun sequencing project
gi|1535930704|gb|RHOS00000000.1|RHO 0000

Nucleotide
Levilactobacillus tangyuanensis strain 137-3, whole genome shotgun sequencing pr...
Levilactobacillus tangyuanensis strain 137-3, whole genome shotgun sequencing project
gi|1535929522|gb|RHOA00000000.1|RHO 0000

Nucleotide
Lapidilactobacillus bayanensis strain 54-5, whole genome shotgun sequencing proj...
Lapidilactobacillus bayanensis strain 54-5, whole genome shotgun sequencing project
gi|1535930972|gb|RHOX00000000.1|RHO 0000

Nucleotide
Companilactobacillus jidongensis strain 204-8, whole genome shotgun sequencing p...
Companilactobacillus jidongensis strain 204-8, whole genome shotgun sequencing project
gi|1535930537|gb|RHOP00000000.1|RHO 0000

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004046917	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance	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

SCV004046917

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004046917.1

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

Description

The missense variant c.1085C>T(p.Thr362Met) in POC1A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Thr362Met variant is novel (not in any individuals) in 1000 Genomes and allele frequency of 0.02653% is reported in gnomAD. The amino acid Thr at position 362 is changed to a Met changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by both SIFT and PolyPhen2. The residue is conserved across species. The amino acid change p.Thr362Met in POC1A is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance. In the absence of another reportable variant the molecular diagnosis is not confirmed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine