SAMD11

protein-coding

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

Gene summary

Predicted to enable several functions, including DNA-binding transcription repressor activity, RNA polymerase II-specific; identical protein binding activity; and protein domain specific binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and retinal rod cell development. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Predicted to be part of PRC1 complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2025]

MANE transcript

NM_001385641.1

Inheritance

ClinVar variants

P:1U:514B:374

Top phenotype

retinitis pigmentosa

gnomAD constraint

pLI —, LoF o/e 0.9

Max pathogenic AF

—

Genomic locus

chr1:923,923-944,575

External References & Databases

Ensembl (ENSG00000187634)

Transcript & Mutation Effects

hg38 • Region Span ~20.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0019200

Submitter: G2P

retinitis pigmentosaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019200

Submitter: Franklin by Genoox

A novel homozygous nonsense mutation in SAMD11 wa found in five individuals diagnosed with adult-onset RP from two unrelated consanguineous Spanish families.

retinitis pigmentosaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019200

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SAMD11 variants in ClinVar

6 Conditions Cataloged

not providedTotal: 1004

not specifiedTotal: 397

SAMD11-related disorderTotal: 55

Retinal dystrophyTotal: 13

Retinitis pigmentosaTotal: 2

Optic atrophyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001385641.1. 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	310 clinvar	6 clinvar	317
missense			458 clinvar	53 clinvar	5 clinvar	516
nonsense		1 clinvar	13 clinvar			14
start loss						0
frameshift			29 clinvar			29
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	1	514	363	11	889

Highest pathogenic variant AF is 0.000048612488

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001385641.1	RefSeq	NP_001372570.1	14	MANE Select
ENST00000616016.5	Ensembl	ENSP00000478421.2	14	MANE Select
NM_001385640.1	RefSeq	NP_001372569.1	14	Standard
NM_152486.4	RefSeq	NP_689699.3	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000342066
Coding exons: 13
Length: 19696
Individuals with no LoFs: 125204
Homozygous LoFs: 11
Heterozygous LoFs: 446
Defined: 125661
p: 0.00182

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-3.44	546	362	1.51	0.0000207	4156
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0051	0.0048	notable
Latino/Admixed American	0.0014	0.0013	notable
Ashkenazi Jewish	0.00061	0.00060	rare
East Asian	0.0085	0.0080	notable
Finnish	0.00050	0.00046	rare
European (Non-Finnish)	0.0012	0.0011	notable
South Asian	0.0011	0.0010	notable
Other	0.0017	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.188

Gene Damage Prediction

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