NM_001162498.3(LPAR6):c.207_210dup (p.Pro71fs) AND Hypotrichosis 8

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 7, 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:: RCV002465046.3

Allele description [Variation Report for NM_001162498.3(LPAR6):c.207_210dup (p.Pro71fs)]

NM_001162498.3(LPAR6):c.207_210dup (p.Pro71fs)

Genes:

RB1:RB transcriptional corepressor 1 [Gene - OMIM - HGNC]
LPAR6:lysophosphatidic acid receptor 6 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

13q14.2

Genomic location:

Preferred name:

NM_001162498.3(LPAR6):c.207_210dup (p.Pro71fs)

HGVS:

NC_000013.11:g.48412214_48412217dup
NG_009009.1:g.113468_113471dup
NG_012874.1:g.37488_37491dup
NG_012874.2:g.37452_37455dup
NM_000321.3:c.1695+30771_1695+30774dupMANE SELECT
NM_001162497.3:c.207_210dup
NM_001162498.3:c.207_210dupMANE SELECT
NM_001377316.2:c.207_210dup
NM_001377317.2:c.207_210dup
NM_001407165.1:c.1695+30771_1695+30774dup
NM_005767.7:c.207_210dup
NP_001155969.1:p.Pro71fs
NP_001155970.1:p.Pro71fs
NP_001364245.1:p.Pro71fs
NP_001364246.1:p.Pro71fs
NP_005758.2:p.Pro71fs
LRG_517:g.113468_113471dup
NC_000013.10:g.48986350_48986353dup

Protein change:

P71fs

Molecular consequence:

NM_001162497.3:c.207_210dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001162498.3:c.207_210dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001377316.2:c.207_210dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001377317.2:c.207_210dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_005767.7:c.207_210dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_000321.3:c.1695+30771_1695+30774dup - intron variant - [Sequence Ontology: SO:0001627]
NM_001407165.1:c.1695+30771_1695+30774dup - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Name:: Hypotrichosis 8 (HYPT8)
Synonyms:: HYPOTRICHOSIS, LOCALIZED, AUTOSOMAL RECESSIVE 3
Identifiers:: MONDO: MONDO:0010206; MedGen: C3279470; Orphanet: 55654; OMIM: 278150

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002759439	Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 7, 2022)	unknown	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

SCV002759439

Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 7, 2022)

unknown

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	unknown	yes	1	1	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 Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology, SCV002759439.1

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

Description

The c.207_210dup variant is not present in publicly available population databases like 1000 Genomes, EVS, ExAC, gnomAD, Indian Exome Database or our in-house exome database. The variant has not been previously reported to ClinVar, Human Genome Mutation Database (HGMD) or OMIM databases in any affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome, Franklin etc. predicted this variant to be likely deleterious. The variant causes frameshift at the 71st amino acid of the wild-type transcript, creating a translational premature stop signal at the 91st amino acid position of the altered transcript, which may either result in translation of a truncated protein or causes nonsense mediated decay of the mRNA.

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

Last Updated: Sep 1, 2024

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