NM_001378454.1(ALMS1):c.10558_10561del (p.Asp3520fs) AND Alstrom syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 8, 2021
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:: RCV001384455.5

Allele description [Variation Report for NM_001378454.1(ALMS1):c.10558_10561del (p.Asp3520fs)]

NM_001378454.1(ALMS1):c.10558_10561del (p.Asp3520fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

2p13.1

Genomic location:

Preferred name:

NM_001378454.1(ALMS1):c.10558_10561del (p.Asp3520fs)

HGVS:

NC_000002.12:g.73572435_73572438del
NG_011690.1:g.191683_191686del
NM_001378454.1:c.10558_10561delMANE SELECT
NM_015120.4:c.10561_10564del
NP_001365383.1:p.Asp3520fs
NP_055935.4:p.Asp3521fs
LRG_741t1:c.10561_10564del
LRG_741:g.191683_191686del
LRG_741p1:p.Asp3521fs
NC_000002.11:g.73799560_73799563del
NC_000002.11:g.73799562_73799565del
NM_015120.4:c.10561_10564delGACA

Protein change:

D3520fs

Links:

dbSNP: rs2104104189

NCBI 1000 Genomes Browser:

rs2104104189

Molecular consequence:

NM_001378454.1:c.10558_10561del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015120.4:c.10561_10564del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001583954	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 8, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17594715, 25846608, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001583954

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 8, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

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

Alström Syndrome: Mutation Spectrum of ALMS1.

Marshall JD, Muller J, Collin GB, Milan G, Kingsmore SF, Dinwiddie D, Farrow EG, Miller NA, Favaretto F, Maffei P, Dollfus H, Vettor R, Naggert JK.

Hum Mutat. 2015 Jul;36(7):660-8. doi: 10.1002/humu.22796. Epub 2015 May 18.

PubMed [citation]

PMID:: 25846608
PMCID:: PMC4475486

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001583954.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Asp3521Asnfs*25) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with Alstrom syndrome (PMID: 25846608). ClinVar contains an entry for this variant (Variation ID: 1071886). For these reasons, this variant has been classified as Pathogenic.

#	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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