NM_000550.3(TYRP1):c.1276C>T (p.Pro426Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 25, 2023
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:: RCV001875240.6

Allele description [Variation Report for NM_000550.3(TYRP1):c.1276C>T (p.Pro426Ser)]

NM_000550.3(TYRP1):c.1276C>T (p.Pro426Ser)

Genes:

LURAP1L-AS1:LURAP1L antisense RNA 1 [Gene - HGNC]
TYRP1:tyrosinase related protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p23

Genomic location:

Preferred name:

NM_000550.3(TYRP1):c.1276C>T (p.Pro426Ser)

HGVS:

NC_000009.12:g.12708011C>T
NG_011705.1:g.19626C>T
NM_000550.3:c.1276C>TMANE SELECT
NP_000541.1:p.Pro426Ser
NC_000009.11:g.12708011C>T

Protein change:

P426S

Links:

dbSNP: rs1273754617

NCBI 1000 Genomes Browser:

rs1273754617

Molecular consequence:

NM_000550.3:c.1276C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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BB414515 RIKEN full-length enriched, 7 days embryo Mus musculus cDNA clone C4300...
BB414515 RIKEN full-length enriched, 7 days embryo Mus musculus cDNA clone C430037P04 3', mRNA sequence
gi|9235870|gnl|dbEST|5333888|dbj|BB 5.1|

Nucleotide
Plekhs1 pleckstrin homology domain containing, family S member 1 [Mus musculus]
Plekhs1 pleckstrin homology domain containing, family S member 1 [Mus musculus]
Gene ID:226245

Gene
226245[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002140408	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 25, 2023)	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

SCV002140408

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 25, 2023)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002140408.3

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

Description

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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TYRP1 protein function. ClinVar contains an entry for this variant (Variation ID: 1373539). This missense change has been observed in individual(s) with clinical features of oculocutaneous albinism (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 426 of the TYRP1 protein (p.Pro426Ser).

#	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: Sep 29, 2024

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