NM_152703.5(SAMD9L):c.3587G>C (p.Cys1196Ser) AND Ataxia-pancytopenia syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Mar 1, 2017
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000234841.1

Allele description

NM_152703.5(SAMD9L):c.3587G>C (p.Cys1196Ser)

Gene:

SAMD9L:sterile alpha motif domain containing 9 like [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q21.2

Genomic location:

Preferred name:

NM_152703.5(SAMD9L):c.3587G>C (p.Cys1196Ser)

HGVS:

NC_000007.14:g.93132385C>G
NG_053186.1:g.21017G>C
NM_001303496.3:c.3587G>C
NM_001303497.3:c.3587G>C
NM_001303498.3:c.3587G>C
NM_001303500.3:c.3587G>C
NM_001350082.2:c.3587G>C
NM_001350083.2:c.3587G>C
NM_001350084.2:c.3587G>C
NM_001350085.2:c.3587G>C
NM_152703.5:c.3587G>CMANE SELECT
NP_001290425.1:p.Cys1196Ser
NP_001290426.1:p.Cys1196Ser
NP_001290427.1:p.Cys1196Ser
NP_001290429.1:p.Cys1196Ser
NP_001337011.1:p.Cys1196Ser
NP_001337012.1:p.Cys1196Ser
NP_001337013.1:p.Cys1196Ser
NP_001337014.1:p.Cys1196Ser
NP_689916.2:p.Cys1196Ser
NC_000007.13:g.92761698C>G
NM_152703.3:c.3587G>C
Q8IVG5:p.Cys1196Ser

Protein change:

C1196S; CYS1196SER

Links:

UniProtKB: Q8IVG5#VAR_077035; OMIM: 611170.0002; dbSNP: rs878855337

NCBI 1000 Genomes Browser:

rs878855337

Molecular consequence:

NM_001303496.3:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001303497.3:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001303498.3:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001303500.3:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001350082.2:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001350083.2:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001350084.2:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001350085.2:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_152703.5:c.3587G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Ataxia-pancytopenia syndrome (ATXPC)
Synonyms:: Myelocerebellar disorder
Identifiers:: MONDO: MONDO:0008038; MedGen: C1327919; OMIM: 159550

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000292028	OMIM	no assertion criteria provided	Pathogenic (Jun 30, 2016)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 283689, 27259050
SCV000611900	GeneReviews	no assertion criteria provided	Pathogenic (Mar 1, 2017)	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 27259050, 28570036
SCV000882878	University of Washington Center for Mendelian Genomics, University of Washington	no assertion criteria provided	Likely pathogenic (Jun 6, 2016)	unknown	research

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000292028

OMIM

no assertion criteria provided

Pathogenic
(Jun 30, 2016)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000611900

GeneReviews

no assertion criteria provided

Pathogenic
(Mar 1, 2017)

germline

literature only

PubMed (2)
[See all records that cite these PMIDs]

SCV000882878

University of Washington Center for Mendelian Genomics, University of Washington

no assertion criteria provided

Likely pathogenic
(Jun 6, 2016)

unknown

research

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only
not provided	unknown	yes	3	not provided	not provided	not provided	not provided	research

Citations

PubMed

A family with acute leukemia, hypoplastic anemia and cerebellar ataxia: association with bone marrow C-monosomy.

Li FP, Potter NU, Buchanan GR, Vawter G, Whang-Peng J, Rosen RB.

Am J Med. 1978 Dec;65(6):933-40.

PubMed [citation]

PMID:: 283689

Ataxia-Pancytopenia Syndrome Is Caused by Missense Mutations in SAMD9L.

Chen DH, Below JE, Shimamura A, Keel SB, Matsushita M, Wolff J, Sul Y, Bonkowski E, Castella M, Taniguchi T, Nickerson D, Papayannopoulou T, Bird TD, Raskind WH.

Am J Hum Genet. 2016 Jun 2;98(6):1146-1158. doi: 10.1016/j.ajhg.2016.04.009.

PubMed [citation]

PMID:: 27259050
PMCID:: PMC4908176

See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000292028.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

Description

In 3 affected members of a Chinese family with ataxia-pancytopenia syndrome (ATXPC; 159550) originally reported by Li et al. (1978), Chen et al. (2016) identified a heterozygous c.3587G-C transversion (c.3587G-C, NM_152703.3) in the SAMD9L gene, resulting in a cys1196-to-ser (C1196S) substitution at a highly conserved residue. The mutation was not found in the dbSNP (build 131), 1000 Genomes Project, or ExAC databases. Functional studies of the variant were not performed. Loss of the variant allele was not observed in cultured fibroblasts from these patients.

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

From GeneReviews, SCV000611900.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (2)

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

From University of Washington Center for Mendelian Genomics, University of Washington, SCV000882878.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	3	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		3	not provided	not provided	not provided

Last Updated: Jun 18, 2022

ClinVar

Relating variation to medicine