SAMD11

sterile alpha motif domain containing 11, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 1:923923-944575

Links

ENSG00000187634 ∙ NCBI:148398 ∙ OMIM:616765 ∙ HGNC:28706 ∙ Uniprot:Q96NU1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• retinitis pigmentosa (Limited), mode of inheritance: AR
• retinitis pigmentosa (Limited), mode of inheritance: AR
• retinitis pigmentosa (Strong), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD11 gene.

• not_provided (944 variants)
• not_specified (191 variants)
• SAMD11-related_disorder (44 variants)
• Retinal_dystrophy (13 variants)
• Retinitis_pigmentosa (2 variants)
• Neutrophil_inclusion_bodies (1 variants)
• Optic_atrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001385641.1. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	262	25	288
missense			443	36	10	489
nonsense	1		11			12
start loss						0
frameshift			27			27
splice donor/acceptor (+/-2bp)			12			12
Total	1	0	494	298	35

Highest pathogenic variant AF is 0.000048612488

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD11	protein_coding	protein_coding	ENST00000342066	13	19696

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.77e-14	0.0502	125204	11	446	125661	0.00182

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-3.44	546	362	1.51	0.0000207	4156
Missense in Polyphen		132	90.043	1.466		1102
Synonymous	-6.92	270	159	1.70	0.00000927	1486
Loss of Function	0.475	22	24.5	0.897	0.00000131	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00654	0.00622
Ashkenazi Jewish	0.000614	0.000596
East Asian	0.00848	0.00797
Finnish	0.000498	0.000462
European (Non-Finnish)	0.00123	0.00114
Middle Eastern	0.00848	0.00797
South Asian	0.00107	0.00105
Other	0.00169	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in photoreceptor development. {ECO:0000250}.

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.264

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.188

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd11

Gene ontology

• Cellular component: nucleus