SAMM50

protein-coding

SAMM50 sorting and assembly machinery component, the group of Mitochondrial sorting and assembly machinery complex

Gene summary

This gene encodes a component of the Sorting and Assembly Machinery (SAM) of the mitochondrial outer membrane. The Sam complex functions in the assembly of beta-barrel proteins into the outer mitochondrial membrane.[provided by RefSeq, Jun 2011]

MANE transcript

NM_015380.5

Inheritance

—

ClinVar variants

U:84B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr22:43,955,442-44,010,531

External References & Databases

Ensembl (ENSG00000100347)

Transcript & Mutation Effects

hg38 • Region Span ~55.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAMM50 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 77

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015380.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar	4 clinvar	6
missense			80 clinvar	4 clinvar		84
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	84	5	4	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015380.5	RefSeq	NP_056195.3	15	MANE Select
ENST00000350028.5	Ensembl	ENSP00000345445.4	15	MANE Select
ENST00000854676.1	Ensembl	ENSP00000524735.1	15	Standard
ENST00000854676.2	Ensembl	ENSP00000524735.1	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Metabolism of proteins
Mitochondrial protein import

Biological Process

mitochondrial respiratory chain complex assembly
cristae formation
protein insertion into mitochondrial outer membrane

Molecular Function

protein binding

Cellular Component

mitochondrial sorting and assembly machinery complex
mitochondrion
mitochondrial outer membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000350028
Coding exons: 15
Length: 55111
Individuals with no LoFs: 125703
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125748
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.915	238	281	0.846	0.0000170	3036
Missense (PolyPhen)		55	85.039	0.64676		817
Synonymous	1.21	89	105	0.850	0.00000680	905
Loss of Function	2.01	18	29.9	0.602	0.00000150	352

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00029	0.00029	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00017	0.00016	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a crucial role in the maintenance of the structure of mitochondrial cristae and the proper assembly of the mitochondrial respiratory chain complexes (PubMed:22252321, PubMed:25781180). Required for the assembly of TOMM40 into the TOM complex (PubMed:15644312). {ECO:0000269|PubMed:15644312, ECO:0000269|PubMed:22252321, ECO:0000269|PubMed:25781180}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

LoFtool: 0.709
RVIS EVS: -0.27
RVIS percentile EVS: 34.82

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.694

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium