NM_000310.4(PPT1):c.541G>A (p.Val181Met) AND Retinitis pigmentosa

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 1, 2021
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:: RCV001723740.3

Allele description [Variation Report for NM_000310.4(PPT1):c.541G>A (p.Val181Met)]

NM_000310.4(PPT1):c.541G>A (p.Val181Met)

Gene:

PPT1:palmitoyl-protein thioesterase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_000310.4(PPT1):c.541G>A (p.Val181Met)

HGVS:

NC_000001.11:g.40080483C>T
NG_009192.1:g.21988G>A
NM_000310.4:c.541G>AMANE SELECT
NM_001142604.2:c.232G>A
NM_001363695.2:c.541G>A
NP_000301.1:p.Val181Met
NP_000301.1:p.Val181Met
NP_001136076.1:p.Val78Met
NP_001350624.1:p.Val181Met
LRG_690t1:c.541G>A
LRG_690:g.21988G>A
LRG_690p1:p.Val181Met
NC_000001.10:g.40546155C>T
NM_000310.3:c.541G>A
P50897:p.Val181Met

Protein change:

V181M

Links:

UniProtKB: P50897#VAR_005557; dbSNP: rs148412181

NCBI 1000 Genomes Browser:

rs148412181

Molecular consequence:

NM_000310.4:c.541G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001142604.2:c.232G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363695.2:c.541G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Retinitis pigmentosa (RP)
Synonyms:: Tapetoretinal degeneration
Identifiers:: MONDO: MONDO:0019200; MeSH: D012174; MedGen: C0035334; Orphanet: 791; OMIM: 268000; OMIM: PS268000

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001950330	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Apr 1, 2021)	germline	curation	PubMed (15) [See all records that cite these PMIDs] 9664077, 10191107, 10649502, 11073228, 11440996, 12796825, 15464427, 19302939, 21499717, 22387303, 23374165, 28878621, 30541466, 25741868, 34906470

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001950330

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Apr 1, 2021)

germline

curation

PubMed (15)
[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	germline	yes	not provided	not provided	not provided	not provided	not provided	curation

Citations

PubMed

Molecular genetics of palmitoyl-protein thioesterase deficiency in the U.S.

Das AK, Becerra CH, Yi W, Lu JY, Siakotos AN, Wisniewski KE, Hofmann SL.

J Clin Invest. 1998 Jul 15;102(2):361-70.

PubMed [citation]

PMID:: 9664077
PMCID:: PMC508894

Genotype-phenotype correlations in neuronal ceroid lipofuscinosis due to palmitoyl-protein thioesterase deficiency.

Hofmann SL, Das AK, Yi W, Lu JY, Wisniewski KE.

Mol Genet Metab. 1999 Apr;66(4):234-9.

PubMed [citation]

PMID:: 10191107

See all PubMed Citations (15)

Details of each submission

From Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard, SCV001950330.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	curation	PubMed (15)

Description

The p.Val181Met variant in PPT1 was identified in an individual with Retinitis pigmentosa, via a collaborative study between the Broad Institute's Center for Mendelian Genomics and the Pierce lab (https://oculargenomics.meei.harvard.edu/labs/pierce-lab/lab-members/). Through a review of available evidence we were able to apply the following criteria: PM2, PP3, PM3, PS3, PP1-M, PM1. Based on this evidence we have classified this variant as Pathogenic. If you have any questions about the classification please reach out to the Pierce Lab.

#	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: Mar 30, 2024

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