NM_000312.4(PROC):c.160A>T (p.Ser54Cys) AND multiple conditions

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Sep 22, 2021
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:
RCV002505135.2

Allele description [Variation Report for NM_000312.4(PROC):c.160A>T (p.Ser54Cys)]

NM_000312.4(PROC):c.160A>T (p.Ser54Cys)

Gene:
PROC:protein C, inactivator of coagulation factors Va and VIIIa [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q14.3
Genomic location:
Preferred name:
NM_000312.4(PROC):c.160A>T (p.Ser54Cys)
Other names:
p.Ser54Cys
HGVS:
  • NC_000002.12:g.127421372A>T
  • NG_016323.1:g.7953A>T
  • NM_000312.4:c.160A>TMANE SELECT
  • NM_001375602.1:c.343A>T
  • NM_001375603.1:c.223A>T
  • NM_001375604.1:c.223A>T
  • NM_001375605.1:c.160A>T
  • NM_001375606.1:c.223A>T
  • NM_001375607.1:c.244A>T
  • NM_001375608.1:c.160A>T
  • NM_001375609.1:c.136A>T
  • NM_001375610.1:c.154A>T
  • NM_001375611.1:c.160A>T
  • NM_001375613.1:c.160A>T
  • NP_000303.1:p.Ser54Cys
  • NP_000303.1:p.Ser54Cys
  • NP_001362531.1:p.Ser115Cys
  • NP_001362532.1:p.Ser75Cys
  • NP_001362533.1:p.Ser75Cys
  • NP_001362534.1:p.Ser54Cys
  • NP_001362535.1:p.Ser75Cys
  • NP_001362536.1:p.Ser82Cys
  • NP_001362537.1:p.Ser54Cys
  • NP_001362538.1:p.Ser46Cys
  • NP_001362539.1:p.Ser52Cys
  • NP_001362540.1:p.Ser54Cys
  • NP_001362542.1:p.Ser54Cys
  • LRG_599t1:c.160A>T
  • LRG_599:g.7953A>T
  • LRG_599p1:p.Ser54Cys
  • NC_000002.11:g.128178948A>T
  • NM_000312.3:c.160A>T
Protein change:
S115C
Links:
dbSNP: rs376049280
NCBI 1000 Genomes Browser:
rs376049280
Molecular consequence:
  • NM_000312.4:c.160A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375602.1:c.343A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375603.1:c.223A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375604.1:c.223A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375605.1:c.160A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375606.1:c.223A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375607.1:c.244A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375608.1:c.160A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375609.1:c.136A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375610.1:c.154A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375611.1:c.160A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375613.1:c.160A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Thrombophilia due to protein C deficiency, autosomal recessive
Synonyms:
PROC DEFICIENCY, AUTOSOMAL RECESSIVE; PROTEIN C DEFICIENCY, AUTOSOMAL RECESSIVE; Thrombophilia, hereditary, due to protein C deficiency, autosomal recessive
Identifiers:
MONDO: MONDO:0012860; MedGen: C2676759; Orphanet: 745; OMIM: 612304
Name:
Thrombophilia due to protein C deficiency, autosomal dominant
Synonyms:
PROC DEFICIENCY, AUTOSOMAL DOMINANT; PROTEIN C DEFICIENCY, AUTOSOMAL DOMINANT; Thrombophilia, hereditary, due to protein C deficiency, autosomal dominant
Identifiers:
MONDO: MONDO:0008316; MedGen: C2674321; Orphanet: 745; OMIM: 176860

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002816192Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 6, 2021) 		unknownclinical testing

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

SCV003920357Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Sep 22, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Fulgent Genetics, Fulgent Genetics, SCV002816192.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV003920357.1

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

Description

PROC NM_000312.3 exon 3 p.Ser54Cys (c.160A>T):This variant has not been reported in the literature in association with disease and is present in 0.01% (15/128944) of European alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/2-127421372-A-T).This variant is present in ClinVar (Variation ID:161338).Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Sep 29, 2024