VCV000008626.1 - ClinVar

NM_020547.3(AMHR2):c.232+1G>A

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_020547.3(AMHR2):c.232+1G>A

Variation ID: 8626 Accession: VCV000008626.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 12q13.13 12: 53424471 (GRCh38) [ NCBI UCSC ] 12: 53818255 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 4, 2013	Apr 4, 2013	Dec 1, 1995

HGVS

Nucleotide	Protein	Molecular consequence
NM_020547.3:c.232+1G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.		splice donor
NM_001164690.2:c.232+1G>A		splice donor
NM_001164691.2:c.232+1G>A		splice donor
NC_000012.12:g.53424471G>A
NC_000012.11:g.53818255G>A
NG_015981.1:g.5617G>A

... more HGVS ... less HGVS

Protein change

Other names

IVS2DS, G-T, +1

Canonical SPDI

NC_000012.12:53424470:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Exome Aggregation Consortium (ExAC) 0.00001

Links

OMIM: 600956.0001 dbSNP: rs763798144 VarSome

Comment on variant

NCBI staff provided an HGVS expression for allelic variant 600956.0001 from the sequence in Figure 4 of the paper by Imbeaud et al., 1995 (PubMed 7493017). There the allele is described as "The G to A mutation".

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
AMHR2		-	-	GRCh38 GRCh37	115	129

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Persistent mullerian duct syndrome, type II	Pathogenic (1)	no assertion criteria provided	Dec 1, 1995	RCV000009158.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Dec 01, 1995)	no assertion criteria provided Method: literature only	PERSISTENT MULLERIAN DUCT SYNDROME, TYPE II Affected status: not provided Allele origin: germline	OMIM Accession: SCV000029375.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 7493017 Comment on evidence: Imbeaud et al. (1995) demonstrated a G-to-A transition at position +1 of the splice donor site of intron 2 of the AMHR gene in a … (more) Imbeaud et al. (1995) demonstrated a G-to-A transition at position +1 of the splice donor site of intron 2 of the AMHR gene in a 3-month-old boy, born to allegedly unrelated Pakistani parents, who came to medical attention because of right cryptorchidism associated with a left inguinal hernia. At surgery, both testes were found in the left scrotum and inguinal canal, associated with a uterus and 2 fallopian tubes (see 261550). Biopsy showed normal seminiferous tubules containing germ cells. Normal regression of fetal rat mullerian ducts was elicited by coculture with a small testicular fragment, thus indicating that AMH was produced. Indeed, the AMH gene was sequenced and found to be normal in this patient. The G-to-A transition they found destroyed an HphI restriction site, allowing the determination of the genotype in the patient and his parents. The mutation was homozygous in the patient and both parents were heterozygotes. The mutation resulted in alternative splicing with production of 2 types of mRNA were produced: the shorter mRNA moiety showed skipping of the second exon with conservation of the reading frame; the longer one contained a 12-bp portion of intron 2, generated by the use of a cryptic donor sequence, GTATA, downstream of the splicing mutation. The result was a gly78-to-asp change of 1 amino acid followed by the insertion of 4 new residues, EWQR, at the end of exon 2. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Insensitivity to anti-müllerian hormone due to a mutation in the human anti-müllerian hormone receptor.	Imbeaud S	Nature genetics	1995	PMID: 7493017

Text-mined citations for rs763798144 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 25, 2023

ClinVar Genomic variation as it relates to human health

NM_020547.3(AMHR2):c.232+1G>A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs763798144 ...