SAMM50

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

Basic information

Region (hg38): 22:43955442-44010531

Links

ENSG00000100347

∙ NCBI:25813 ∙ OMIM:612058 ∙ HGNC:24276 ∙ Uniprot:Q9Y512 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMM50 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMM50 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					5 clinvar	5
missense			40 clinvar	2 clinvar		42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	2	5

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMM50	protein_coding	protein_coding	ENST00000350028	15	55111

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.88e-9	0.953	125703	0	45	125748	0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.915	238	281	0.846	0.0000170	3036
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000659	0.000659
Ashkenazi Jewish	0.0000997	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000172	0.000163
Other	0.000326	0.000326

dbNSFP

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}.;
Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

pRec: 0.121

Intolerance Scores

loftool: 0.709
rvis_EVS: -0.27
rvis_percentile_EVS: 34.82

Haploinsufficiency Scores

pHI: 0.103
hipred: N
hipred_score: 0.414
ghis: 0.620

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Samm50
Phenotype

Gene ontology

Biological process: mitochondrial respiratory chain complex assembly;cristae formation;protein insertion into mitochondrial outer membrane
Cellular component: mitochondrial sorting and assembly machinery complex;mitochondrion;mitochondrial outer membrane;integral component of membrane;extracellular exosome
Molecular function: protein binding