NM_006017.3(PROM1):c.155T>C (p.Ile52Thr) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 24, 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:: RCV001850847.6

Allele description [Variation Report for NM_006017.3(PROM1):c.155T>C (p.Ile52Thr)]

NM_006017.3(PROM1):c.155T>C (p.Ile52Thr)

Gene:

PROM1:prominin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p15.32

Genomic location:

Preferred name:

NM_006017.3(PROM1):c.155T>C (p.Ile52Thr)

HGVS:

NC_000004.12:g.16075752A>G
NG_011696.2:g.13308T>C
NM_001145847.2:c.155T>C
NM_001145848.2:c.155T>C
NM_001145849.2:c.155T>C
NM_001145850.2:c.155T>C
NM_001145851.2:c.155T>C
NM_001145852.2:c.155T>C
NM_001371406.1:c.155T>C
NM_001371407.1:c.155T>C
NM_001371408.1:c.155T>C
NM_006017.3:c.155T>CMANE SELECT
NP_001139319.1:p.Ile52Thr
NP_001139320.1:p.Ile52Thr
NP_001139321.1:p.Ile52Thr
NP_001139322.1:p.Ile52Thr
NP_001139323.1:p.Ile52Thr
NP_001139324.1:p.Ile52Thr
NP_001358335.1:p.Ile52Thr
NP_001358336.1:p.Ile52Thr
NP_001358337.1:p.Ile52Thr
NP_006008.1:p.Ile52Thr
NP_006008.1:p.Ile52Thr
NC_000004.11:g.16077375A>G
NG_011696.1:g.13249T>C
NM_006017.2:c.155T>C

Protein change:

I52T

Links:

dbSNP: rs778896066

NCBI 1000 Genomes Browser:

rs778896066

Molecular consequence:

NM_001145847.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145848.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145849.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145850.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145851.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001145852.2:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001371406.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001371407.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001371408.1:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_006017.3:c.155T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002302142	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 24, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30215852, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002302142

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 24, 2022)

germline

clinical testing

PubMed (2)
[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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Genetic screening for macular dystrophies in patients clinically diagnosed with dry age-related macular degeneration.

Kersten E, Geerlings MJ, Pauper M, Corominas J, Bakker B, Altay L, Fauser S, de Jong EK, Hoyng CB, den Hollander AI.

Clin Genet. 2018 Dec;94(6):569-574. doi: 10.1111/cge.13447. Epub 2018 Oct 15.

PubMed [citation]

PMID:: 30215852
PMCID:: PMC6282796

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, SCV002302142.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

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 PROM1 protein function. ClinVar contains an entry for this variant (Variation ID: 348010). This missense change has been observed in individual(s) with dry age-related macular degeneration (PMID: 30215852). This variant is present in population databases (rs778896066, gnomAD 0.03%). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 52 of the PROM1 protein (p.Ile52Thr).

#	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: Nov 10, 2024

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