NM_000539.3(RHO):c.329G>T (p.Cys110Phe) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: May 30, 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:: RCV003553893.1

Allele description [Variation Report for NM_000539.3(RHO):c.329G>T (p.Cys110Phe)]

NM_000539.3(RHO):c.329G>T (p.Cys110Phe)

Gene:

RHO:rhodopsin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q22.1

Genomic location:

Preferred name:

NM_000539.3(RHO):c.329G>T (p.Cys110Phe)

HGVS:

NC_000003.12:g.129529062G>T
NG_009115.1:g.5424G>T
NG_100653.1:g.573G>T
NM_000539.3:c.329G>TMANE SELECT
NP_000530.1:p.Cys110Phe
NC_000003.11:g.129247905G>T

Protein change:

C110F

Molecular consequence:

NM_000539.3:c.329G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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RecName: Full=Tyrosyl-DNA phosphodiesterase 2; Short=Tyr-DNA phosphodiesterase 2...
RecName: Full=Tyrosyl-DNA phosphodiesterase 2; Short=Tyr-DNA phosphodiesterase 2; Short=hTDP2; AltName: Full=5'-tyrosyl-DNA phosphodiesterase; Short=5'-Tyr-DNA phosphodiesterase; AltName: Full=ETS1-associated protein 2; AltName: Full=ETS1-associated protein II; Short=EAPII; AltName: Full=TRAF and TNF receptor-associated protein; AltName: Full=Tyrosyl-RNA phosphodiesterase; AltName: Full=VPg unlinkase
gi|67462008|sp|O95551.1|TYDP2_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004293486	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (May 30, 2023)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 8088850, 9810568, 30240733, 10051572, 19913029, 30977563, 7981701, 11139241, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004293486

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(May 30, 2023)

germline

clinical testing

PubMed (9)
[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

Further screening of the rhodopsin gene in patients with autosomal dominant retinitis pigmentosa.

Vaithinathan R, Berson EL, Dryja TP.

Genomics. 1994 May 15;21(2):461-3. No abstract available.

PubMed [citation]

PMID:: 8088850

Rhodopsin C110Y mutation causes a type 2 autosomal dominant retinitis pigmentosa.

Millá E, Héon E, Grounauer PA, Piguet B, Ducrey N, Stone EM, Schorderet DF, Munier FL.

Ophthalmic Genet. 1998 Sep;19(3):131-9.

PubMed [citation]

PMID:: 9810568

See all PubMed Citations (9)

Details of each submission

From Invitae, SCV004293486.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Cys110 amino acid residue in RHO. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8088850, 9810568, 19913029, 30240733). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects RHO function (PMID: 10051572, 19913029, 30977563). 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 expected to disrupt RHO protein function. This missense change has been observed in individuals with autosomal dominant retinitis pigmentosa (PMID: 7981701, 11139241). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with phenylalanine, which is neutral and non-polar, at codon 110 of the RHO protein (p.Cys110Phe).

#	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: Feb 20, 2024

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