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NM_001278431.2(C1QTNF5):c.489C>G (p.Ser163Arg) AND Late-onset retinal degeneration

Germline classification:
Pathogenic/Likely pathogenic (4 submissions)
Last evaluated:
Aug 17, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000002208.7

Allele description [Variation Report for NM_001278431.2(C1QTNF5):c.489C>G (p.Ser163Arg)]

NM_001278431.2(C1QTNF5):c.489C>G (p.Ser163Arg)

Genes:
C1QTNF5:C1q and TNF related 5 [Gene - OMIM - HGNC]
MFRP:membrane frizzled-related protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11q23.3
Genomic location:
Preferred name:
NM_001278431.2(C1QTNF5):c.489C>G (p.Ser163Arg)
Other names:
C1QTNF5, SER163ARG
HGVS:
  • NC_000011.10:g.119339574G>C
  • NG_012235.1:g.12100C>G
  • NM_001278431.2:c.489C>GMANE SELECT
  • NM_015645.5:c.489C>G
  • NM_031433.4:c.*1385C>GMANE SELECT
  • NP_001265360.1:p.Ser163Arg
  • NP_056460.1:p.Ser163Arg
  • NC_000011.9:g.119210284G>C
  • NM_001278431.1:c.489C>G
  • NM_015645.3:c.489C>G
  • NM_015645.4:c.489C>G
  • Q9BXJ0:p.Ser163Arg
Protein change:
S163R; SER163ARG
Links:
UniProtKB: Q9BXJ0#VAR_032629; OMIM: 608752.0001; dbSNP: rs111033578
NCBI 1000 Genomes Browser:
rs111033578
Molecular consequence:
  • NM_031433.4:c.*1385C>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001278431.2:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_015645.5:c.489C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Late-onset retinal degeneration (LORD)
Synonyms:
RETINAL DEGENERATION, LATE-ONSET, AUTOSOMAL DOMINANT
Identifiers:
MONDO: MONDO:0011579; MedGen: C1854065; Orphanet: 67042; OMIM: 605670

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022366OMIM
no assertion criteria provided
Pathogenic
(Oct 15, 2003)
germlineliterature only

PubMed (1)
[See all records that cite this PMID]

SCV000255333UCLA Clinical Genomics Center, UCLA - CES
criteria provided, single submitter

(Lee et al. (JAMA. 2014))
Likely pathogenic
(Jun 12, 2012)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001760265Genomics England Pilot Project, Genomics England
no assertion criteria provided

(ACGS Guidelines, 2016)
Pathogenicgermlineclinical testing

Citation Link,

SCV004032299Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 17, 2023)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
European Caucasian (Norway)unknownyesnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Mutation in a short-chain collagen gene, CTRP5, results in extracellular deposit formation in late-onset retinal degeneration: a genetic model for age-related macular degeneration.

Hayward C, Shu X, Cideciyan AV, Lennon A, Barran P, Zareparsi S, Sawyer L, Hendry G, Dhillon B, Milam AH, Luthert PJ, Swaroop A, Hastie ND, Jacobson SG, Wright AF.

Hum Mol Genet. 2003 Oct 15;12(20):2657-67. Epub 2003 Aug 27.

PubMed [citation]
PMID:
12944416

Clinical exome sequencing for genetic identification of rare Mendelian disorders.

Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, Das K, Toy T, Harry B, Yourshaw M, Fox M, Fogel BL, Martinez-Agosto JA, Wong DA, Chang VY, Shieh PB, Palmer CG, Dipple KM, Grody WW, Vilain E, Nelson SF.

JAMA. 2014 Nov 12;312(18):1880-7. doi: 10.1001/jama.2014.14604.

PubMed [citation]
PMID:
25326637
PMCID:
PMC4278636
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000022366.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In affected members of 7 unrelated families with late-onset retinal degeneration (LORD; 605670), Hayward et al. (2003) described a C-to-G transversion at nucleotide 686 in exon 3 of the CTRP5 gene that resulted in a ser163-to-arg (S163R) amino acid substitution. The affected members of these 7 Scottish and North American families shared a 3-Mb haplotype on chromosome 11q23, suggesting a founder effect. The highly evolutionarily conserved serine-163 lies in the carboxy-terminal C1q region, a region which is thought to be essential for trimerization of the collagen domain. Biochemical studies revealed a propensity for high molecular weight aggregates of the mutant protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From UCLA Clinical Genomics Center, UCLA - CES, SCV000255333.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1European Caucasian (Norway)not providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Genomics England Pilot Project, Genomics England, SCV001760265.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV004032299.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Criteria applied: PS1,PS3,PS4_MOD,PM1_SUP,PM2_SUP,PP3

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024