NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln) AND Aganglionic megacolon

Germline classification:: no classifications from unflagged records (2 submissions)
Last evaluated:: Aug 1, 2024
Review status:: no classifications from unflagged records

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:: RCV000627055.4

Allele description [Variation Report for NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln)]

NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln)

Gene:

SEMA3D:semaphorin 3D [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.11

Genomic location:

Preferred name:

NM_001384900.1(SEMA3D):c.1272C>A (p.His424Gln)

HGVS:

NC_000007.14:g.85022533G>T
NG_051329.1:g.169323C>A
NM_001384900.1:c.1272C>AMANE SELECT
NM_001384901.1:c.1272C>A
NM_001384902.1:c.1272C>A
NM_001384903.1:c.1272C>A
NM_152754.3:c.1272C>A
NP_001371829.1:p.His424Gln
NP_001371830.1:p.His424Gln
NP_001371831.1:p.His424Gln
NP_001371832.1:p.His424Gln
NP_689967.2:p.His424Gln
NP_689967.2:p.His424Gln
NC_000007.13:g.84651849G>T
NM_152754.2:c.1272C>A
p.(His424Gln)

Protein change:

H424Q

Links:

dbSNP: rs141893504

NCBI 1000 Genomes Browser:

rs141893504

Molecular consequence:

NM_001384900.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384901.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384902.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001384903.1:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152754.3:c.1272C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Aganglionic megacolon (HSCR)
Synonyms:: Hirschsprung's disease; Hirschsprung disease
Identifiers:: MONDO: MONDO:0018309; MeSH: D006627; MedGen: C0019569; Orphanet: 388; OMIM: PS142623; Human Phenotype Ontology: HP:0002251

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No clinical assertions found. See "Flagged submissions" below.

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	research
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 Center of Genomic medicine, Geneva, University Hospital of Geneva, SCV000747763.2

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

Description

This variant was identified in a patient with Hirschsprung disease and a positive familial history. The patient harbours also a variant in the RET gene, which is a risk factor for this disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Human Genomics Unit, Institute for molecular medicine Finland (FIMM), SCV000845749.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	research	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000747763	Center of Genomic medicine, Geneva, University Hospital of Geneva	flagged submission Reason: Outlier claim with insufficient supporting evidence Notes: None (ACMG Guidelines, 2015)	Uncertain significance (Nov 20, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000845749	Human Genomics Unit, Institute for molecular medicine Finland (FIMM)	flagged submission Reason: Outlier claim with insufficient supporting evidence Notes: None	Likely pathogenic	unknown	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000747763

Center of Genomic medicine, Geneva, University Hospital of Geneva

flagged submission

Reason: Outlier claim with insufficient supporting evidence

Notes: None

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 20, 2017)

germline

clinical testing

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

SCV000845749

Human Genomics Unit, Institute for molecular medicine Finland (FIMM)

flagged submission

Reason: Outlier claim with insufficient supporting evidence

Notes: None

Likely pathogenic

unknown

research

Last Updated: Nov 3, 2024

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