NM_001378454.1(ALMS1):c.10930C>G (p.Leu3644Val) AND Alstrom syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 10, 2016
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:: RCV000460490.6

Allele description [Variation Report for NM_001378454.1(ALMS1):c.10930C>G (p.Leu3644Val)]

NM_001378454.1(ALMS1):c.10930C>G (p.Leu3644Val)

Gene:

ALMS1:ALMS1 centrosome and basal body associated protein [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.1

Genomic location:

Preferred name:

NM_001378454.1(ALMS1):c.10930C>G (p.Leu3644Val)

HGVS:

NC_000002.12:g.73572807C>G
NG_011690.1:g.192055C>G
NM_001378454.1:c.10930C>GMANE SELECT
NM_015120.4:c.10933C>G
NP_001365383.1:p.Leu3644Val
NP_055935.4:p.Leu3645Val
LRG_741t1:c.10933C>G
LRG_741:g.192055C>G
LRG_741p1:p.Leu3645Val
NC_000002.11:g.73799934C>G

Protein change:

L3644V

Links:

dbSNP: rs1060500033

NCBI 1000 Genomes Browser:

rs1060500033

Molecular consequence:

NM_001378454.1:c.10930C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_015120.4:c.10933C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Alstrom syndrome (ALMS)
Synonyms:: Alstrom's syndrome
Identifiers:: MONDO: MONDO:0008763; MedGen: C0268425; Orphanet: 64; OMIM: 203800

Recent activity

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unnamed protein product [Aspergillus oryzae RIB40]
unnamed protein product [Aspergillus oryzae RIB40]
gi|1300547054|ref|XP_023090838.1|

Protein
zinc finger CCHC domain-containing protein 2 isoform B [Mus musculus]
zinc finger CCHC domain-containing protein 2 isoform B [Mus musculus]
gi|170016071|ref|NP_001116147.1|

Protein
Arabidopsis thaliana DNA binding protein (AT1G36095), partial mRNA
Arabidopsis thaliana DNA binding protein (AT1G36095), partial mRNA
gi|18400016|ref|NM_103306.1|

Nucleotide
Homo sapiens general transcription factor IIIC, polypeptide 5, 63kDa, mRNA (cDNA...
Homo sapiens general transcription factor IIIC, polypeptide 5, 63kDa, mRNA (cDNA clone MGC:18246 IMAGE:4157684), complete cds
gi|15030195|gb|BC011355.1|

Nucleotide
serrate RNA effector molecule [Cucumis sativus]
serrate RNA effector molecule [Cucumis sativus]
gi|449452662|ref|XP_004144078.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000541329	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 10, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000541329

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 10, 2016)

germline

clinical testing

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000541329.4

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

Description

This sequence change replacesleucine with valine at codon 3645 of the ALMS1 protein (p.Leu3645Val). The leucine residue is highly conserved and there is a small physicochemical difference between leucine and valine. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a ALMS1-related disease. In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.

#	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

Last Updated: Sep 29, 2024

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