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 (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.

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			2	246	25	273
missense			419	22	12	453
nonsense	1		10			11
start loss						0
frameshift			24			24
inframe indel			12			12
splice donor/acceptor (+/-2bp)			12			12
splice region			11	24	6	41
non coding			16	120	17	153
Total	1	0	495	388	54

Variants in SAMD11

This is a list of pathogenic ClinVar variants found in the SAMD11 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-924518-G-C			Likely benign (Oct 01, 2024)
1-925946-C-G			Uncertain significance (Feb 23, 2022)
1-925952-G-A			Uncertain significance (Mar 10, 2022)
1-925956-C-T			Likely benign (Nov 29, 2024)
1-925961-A-T			Uncertain significance (Dec 24, 2021)
1-925969-C-T			Likely benign (Jan 18, 2025)
1-925976-T-C		not specified	Uncertain significance (Mar 01, 2025)
1-925980-C-T			Likely benign (Mar 29, 2021)
1-925986-C-T			Likely benign (Jul 05, 2022)
1-926003-C-T			Uncertain significance (Feb 03, 2025)
1-926010-G-T			Likely benign (Feb 08, 2024)
1-926014-G-A			Uncertain significance (Aug 24, 2021)
1-926018-G-A			Uncertain significance (May 17, 2022)
1-926025-G-A			Likely benign (Oct 03, 2024)
1-926026-G-A			Likely benign (Sep 20, 2022)
1-926026-G-T			Likely benign (Jan 09, 2023)
1-926027-C-T			Likely benign (Jan 15, 2025)
1-926029-C-T			Likely benign (Jul 19, 2022)
1-930081-AGCCCCACCTTCCTCTCCTCCT-A		SAMD11-related disorder	Likely benign (May 28, 2019)
1-930136-T-C			Likely benign (Mar 18, 2021)
1-930136-TCTC-T			Likely benign (Apr 03, 2024)
1-930139-C-T			Likely benign (Dec 02, 2024)
1-930158-C-T			Uncertain significance (Oct 25, 2024)
1-930163-G-A		SAMD11-related disorder	Likely benign (Dec 12, 2024)
1-930164-C-T			Uncertain significance (Jun 15, 2022)

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