NM_001162498.3(LPAR6):c.830T>C (p.Leu277Pro) AND Hypotrichosis 8

Germline classification:: Likely pathogenic (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:: RCV003234611.1

Allele description [Variation Report for NM_001162498.3(LPAR6):c.830T>C (p.Leu277Pro)]

NM_001162498.3(LPAR6):c.830T>C (p.Leu277Pro)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

13q14.2

Genomic location:

Preferred name:

NM_001162498.3(LPAR6):c.830T>C (p.Leu277Pro)

HGVS:

NC_000013.11:g.48411594A>G
NG_009009.1:g.112848A>G
NG_012874.2:g.38075T>C
NG_127784.1:g.98A>G
NM_000321.3:c.1695+30151A>GMANE SELECT
NM_001162497.3:c.830T>C
NM_001162498.3:c.830T>CMANE SELECT
NM_001377316.2:c.830T>C
NM_001377317.2:c.830T>C
NM_001407165.1:c.1695+30151A>G
NM_005767.7:c.830T>C
NP_001155969.1:p.Leu277Pro
NP_001155970.1:p.Leu277Pro
NP_001364245.1:p.Leu277Pro
NP_001364246.1:p.Leu277Pro
NP_005758.2:p.Leu277Pro
LRG_517:g.112848A>G
NC_000013.10:g.48985730A>G
NG_012874.1:g.38111T>C

Protein change:

L277P

Molecular consequence:

NM_000321.3:c.1695+30151A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407165.1:c.1695+30151A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001162497.3:c.830T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001162498.3:c.830T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377316.2:c.830T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001377317.2:c.830T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005767.7:c.830T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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Profile neighbors for GEO Profiles (Select 132554102) (199)
GEO Profiles
BAI1-associated protein 3 isoform X3 [Homo sapiens]
BAI1-associated protein 3 isoform X3 [Homo sapiens]
gi|767987812|ref|XP_011521032.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003932429	SIB Swiss Institute of Bioinformatics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	unknown	curation	PubMed (3) [See all records that cite these PMIDs] 19292720, 36173926, 25741868

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003932429

SIB Swiss Institute of Bioinformatics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

unknown

curation

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Mutations in the P2RY5 gene underlie autosomal recessive hypotrichosis in 13 Pakistani families.

Tariq M, Ayub M, Jelani M, Basit S, Naz G, Wasif N, Raza SI, Naveed AK, ullah Khan S, Azeem Z, Yasinzai M, Wali A, Ali G, Chishti MS, Ahmad W.

Br J Dermatol. 2009 May;160(5):1006-10. doi: 10.1111/j.1365-2133.2009.09046.x. Epub 2009 Mar 9.

PubMed [citation]

PMID:: 19292720

Cell-trafficking impairment in disease-associated LPA6 missense mutants and a potential pharmacoperone therapy for autosomal recessive woolly hair/hypotrichosis.

Yanagida K, Masago K, Yasuda D, Hamano F, Kurikawa Y, Shimizu T, Ishii S.

Hum Mol Genet. 2023 Feb 19;32(5):825-834. doi: 10.1093/hmg/ddac244.

PubMed [citation]

PMID:: 36173926

See all PubMed Citations (3)

Details of each submission

From SIB Swiss Institute of Bioinformatics, SCV003932429.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (3)

Description

This variant is interpreted as likely pathogenic for Hypotrichosis 8, autosomal recessive. The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (PM2); Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PP1 upgraded to strong); For recessive disorders, detected in trans with a pathogenic variant (PM3 downgraded to supporting); Well-established functional studies show a deleterious effect (PS3 downgraded to supporting); Multiple lines of computational evidence support a deleterious effect on the gene or gene product (PP3).

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

Last Updated: Sep 1, 2024

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