NM_001378454.1(ALMS1):c.6553C>T (p.Pro2185Ser) AND Alstrom syndrome

Clinical significance:Benign (Last evaluated: Nov 1, 2022)
Review status:2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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Based on:: 4 submissions [Details]
Record status:: current
Accession:: RCV000226842.21

Allele description [Variation Report for NM_001378454.1(ALMS1):c.6553C>T (p.Pro2185Ser)]

NM_001378454.1(ALMS1):c.6553C>T (p.Pro2185Ser)

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.6553C>T (p.Pro2185Ser)

HGVS:

NC_000002.12:g.73453080C>T
NG_011690.1:g.72328C>T
NM_001378454.1:c.6553C>TMANE SELECT
NM_015120.4:c.6556C>T
NP_001365383.1:p.Pro2185Ser
NP_055935.4:p.Pro2186Ser
LRG_741t1:c.6556C>T
LRG_741:g.72328C>T
LRG_741p1:p.Pro2186Ser
NC_000002.11:g.73680207C>T
p.Pro2184Ser

Protein change:

P2185S

Links:

dbSNP: rs77555300

NCBI 1000 Genomes Browser:

rs77555300

Molecular consequence:

NM_001378454.1:c.6553C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_015120.4:c.6556C>T - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000290101	Invitae	criteria provided, single submitter Invitae Variant Classification Sherloc (09022015)	Benign (Nov 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002082833	Natera, Inc.	no assertion criteria provided	Benign (Dec 2, 2019)	germline	clinical testing
SCV002506091	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter ARUP Molecular Germline Variant Investigation Process 2021	Benign (Feb 8, 2022)	germline	clinical testing	Citation Link,
SCV002605261	Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic	criteria provided, single submitter K & H Uppaluri Personalized Medicine Clinic Variant Classification & Assertion Criteria_Updated V.1	Benign	unknown	research	PubMed (4) [See all records that cite these PMIDs] 34148947, 25846608, 30421101, 33669459 Citation Link

Summary from all submissions

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Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	research
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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Novel Mutations of the ALMS1 Gene in Patients with Alström Syndrome.

Wang C, Luo X, Wang Y, Liu Z, Wu S, Wang S, Lan X, Xu Q, Xu W, Yuan F, Wang A, Zeng F, Jia J, Chen Y.

Intern Med. 2021 Dec 1;60(23):3721-3728. doi: 10.2169/internalmedicine.6467-20. Epub 2021 Jun 19.

PubMed [citation]

PMID:: 34148947
PMCID:: PMC8710367

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV000290101.9

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

#	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 Natera, Inc., SCV002082833.1

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

#	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002506091.2

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

#	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 Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic, SCV002605261.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		not provided	not provided	not provided	research	PubMed (4)

Description

Potent mutations in ALMS1 are associated with a rare condition called Alstrom syndrome. It can cause excessive eating, insulin resistance. However, no evidence is found to ascertain the role of rs77555300 in Alstrom syndrome yet.

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

Last Updated: Mar 4, 2023

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