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NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly) AND Microcephaly-capillary malformation syndrome

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Jun 7, 2022
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:
RCV001808859.4

Allele description [Variation Report for NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly)]

NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly)

Genes:
LOC126806253:CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:74057585-74058784 [Gene]
STAMBP:STAM binding protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p13.1
Genomic location:
Preferred name:
NM_213622.4(STAMBP):c.112C>G (p.Arg38Gly)
HGVS:
  • NC_000002.12:g.73830968C>G
  • NG_033223.2:g.7058C>G
  • NM_001353967.2:c.112C>G
  • NM_001353968.2:c.112C>G
  • NM_001353969.2:c.112C>G
  • NM_001353970.2:c.112C>G
  • NM_001353971.2:c.-442C>G
  • NM_001353972.2:c.-203+1972C>G
  • NM_001353973.2:c.-442C>G
  • NM_001353974.2:c.-442C>G
  • NM_001353975.2:c.-442C>G
  • NM_001353976.2:c.-442C>G
  • NM_006463.6:c.112C>G
  • NM_201647.4:c.112C>G
  • NM_213622.4:c.112C>GMANE SELECT
  • NP_001340896.1:p.Arg38Gly
  • NP_001340897.1:p.Arg38Gly
  • NP_001340898.1:p.Arg38Gly
  • NP_001340899.1:p.Arg38Gly
  • NP_006454.1:p.Arg38Gly
  • NP_964010.1:p.Arg38Gly
  • NP_998787.1:p.Arg38Gly
  • NC_000002.11:g.74058095C>G
  • NR_148668.2:n.160C>G
  • NR_148669.2:n.160C>G
  • NR_148670.2:n.340C>G
  • NR_148671.2:n.674C>G
Protein change:
R38G
Links:
dbSNP: rs143739249
NCBI 1000 Genomes Browser:
rs143739249
Molecular consequence:
  • NM_001353971.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353973.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353974.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353975.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353976.2:c.-442C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001353972.2:c.-203+1972C>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353967.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353968.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353969.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001353970.2:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006463.6:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_201647.4:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_213622.4:c.112C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148668.2:n.160C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148669.2:n.160C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148670.2:n.340C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148671.2:n.674C>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
2

Condition(s)

Name:
Microcephaly-capillary malformation syndrome (MICCAP)
Identifiers:
MONDO: MONDO:0013659; MedGen: C3280296; Orphanet: 294016; OMIM: 614261

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV0020590413billion
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jan 3, 2022) 		germlineclinical testing

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

SCV002580856MGZ Medical Genetics Center
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Jun 7, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot provided1not 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 3billion, SCV002059041.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000050793, PM5_M). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.863, PP3_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From MGZ Medical Genetics Center, SCV002580856.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024