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NM_001378454.1(ALMS1):c.7866C>A (p.Cys2622Ter) AND Alstrom syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 14, 2022
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:
RCV003024045.3

Allele description [Variation Report for NM_001378454.1(ALMS1):c.7866C>A (p.Cys2622Ter)]

NM_001378454.1(ALMS1):c.7866C>A (p.Cys2622Ter)

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.7866C>A (p.Cys2622Ter)
HGVS:
  • NC_000002.12:g.73489825C>A
  • NG_011690.1:g.109073C>A
  • NM_001378454.1:c.7866C>AMANE SELECT
  • NM_015120.4:c.7869C>A
  • NP_001365383.1:p.Cys2622Ter
  • NP_055935.3:p.Cys2623Ter
  • NP_055935.4:p.Cys2623Ter
  • LRG_741t1:c.7869C>A
  • LRG_741:g.109073C>A
  • LRG_741p1:p.Cys2623Ter
  • NC_000002.11:g.73716952C>A
  • NM_015120.3:c.7869C>A
Protein change:
C2622*
Molecular consequence:
  • NM_001378454.1:c.7866C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_015120.4:c.7869C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003324059Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 14, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Spectrum of ALMS1 variants and evaluation of genotype-phenotype correlations in Alström syndrome.

Marshall JD, Hinman EG, Collin GB, Beck S, Cerqueira R, Maffei P, Milan G, Zhang W, Wilson DI, Hearn T, Tavares P, Vettor R, Veronese C, Martin M, So WV, Nishina PM, Naggert JK.

Hum Mutat. 2007 Nov;28(11):1114-23.

PubMed [citation]
PMID:
17594715

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, SCV003324059.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ALMS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys2623*) in the ALMS1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ALMS1 are known to be pathogenic (PMID: 17594715).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024