NM_002834.5(PTPN11):c.172A>G (p.Asn58Asp) AND Male infertility with azoospermia or oligozoospermia due to single gene mutation

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 1, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003991571.1

Allele description [Variation Report for NM_002834.5(PTPN11):c.172A>G (p.Asn58Asp)]

NM_002834.5(PTPN11):c.172A>G (p.Asn58Asp)

Gene:

PTPN11:protein tyrosine phosphatase non-receptor type 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q24.13

Genomic location:

Preferred name:

NM_002834.5(PTPN11):c.172A>G (p.Asn58Asp)

Other names:

p.N58D:AAC>GAC

HGVS:

NC_000012.12:g.112450352A>G
NG_007459.1:g.36621A>G
NM_001330437.2:c.172A>G
NM_001374625.1:c.169A>G
NM_002834.5:c.172A>GMANE SELECT
NM_080601.3:c.172A>G
NP_001317366.1:p.Asn58Asp
NP_001361554.1:p.Asn57Asp
NP_002825.3:p.Asn58Asp
NP_542168.1:p.Asn58Asp
LRG_614t1:c.172A>G
LRG_614:g.36621A>G
NC_000012.11:g.112888156A>G
NM_001330437.1:c.172A>G
NM_002834.3:c.172A>G
NM_002834.4:c.172A>G
c.172A>G

Protein change:

N57D

Links:

dbSNP: rs397507505

NCBI 1000 Genomes Browser:

rs397507505

Molecular consequence:

NM_001330437.2:c.172A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001374625.1:c.169A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_002834.5:c.172A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_080601.3:c.172A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Male infertility with azoospermia or oligozoospermia due to single gene mutation
Identifiers:: MedGen: C5681165

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004231710	Laan Lab, Human Genetics Research Group, University of Tartu	criteria provided, single submitter (Gelb et al. (Genet Med. 2018))	Pathogenic (Dec 1, 2023)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004231710

Laan Lab, Human Genetics Research Group, University of Tartu

criteria provided, single submitter

(Gelb et al. (Genet Med. 2018))

Pathogenic
(Dec 1, 2023)

germline

research

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

ClinGen's RASopathy Expert Panel consensus methods for variant interpretation.

Gelb BD, Cavé H, Dillon MW, Gripp KW, Lee JA, Mason-Suares H, Rauen KA, Williams B, Zenker M, Vincent LM; ClinGen RASopathy Working Group..

Genet Med. 2018 Nov;20(11):1334-1345. doi: 10.1038/gim.2018.3. Epub 2018 Mar 1.

PubMed [citation]

PMID:: 29493581
PMCID:: PMC6119537

Details of each submission

From Laan Lab, Human Genetics Research Group, University of Tartu, SCV004231710.1

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

#	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		1	not provided	not provided	not provided

Last Updated: Nov 3, 2024

ClinVar

Relating variation to medicine