SAMD7

sterile alpha motif domain containing 7, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 3:169911572-169939175

Links

ENSG00000187033 ∙ NCBI:344658 ∙ ∙ HGNC:25394 ∙ Uniprot:Q7Z3H4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• macular dystrophy with or without cone dysfunction (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Macular dystrophy with or without cone dysfunction	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	38272031

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAMD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAMD7 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						0
missense			26	2		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	0

Variants in SAMD7

This is a list of pathogenic ClinVar variants found in the SAMD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-169919505-G-A		not specified	Likely benign (Jul 17, 2023)
3-169919527-C-T		not specified	Uncertain significance (May 16, 2023)
3-169921219-T-C		not specified	Uncertain significance (Nov 24, 2024)
3-169921233-G-A		not specified	Uncertain significance (Oct 09, 2024)
3-169921306-T-C		not specified	Uncertain significance (Apr 15, 2024)
3-169921327-G-A		not specified	Uncertain significance (Nov 13, 2024)
3-169921339-G-A		Macular dystrophy with or without cone dysfunction	Pathogenic (Mar 19, 2024)
3-169925110-A-T		not specified	Uncertain significance (Mar 01, 2025)
3-169925121-G-A		not specified	Uncertain significance (Nov 22, 2022)
3-169925137-G-A		MACULAR DYSTROPHY WITH CONE DYSFUNCTION	Pathogenic (Mar 18, 2024)
3-169926584-C-G		not specified	Uncertain significance (Feb 18, 2025)
3-169926629-G-A		not specified	Uncertain significance (Aug 26, 2024)
3-169926668-C-T		not specified	Uncertain significance (Oct 21, 2024)
3-169926672-C-A		not specified	Uncertain significance (Jul 21, 2021)
3-169926688-G-C		not specified	Uncertain significance (Feb 26, 2024)
3-169926714-A-G		not specified	Uncertain significance (Jun 26, 2023)
3-169926753-C-T		not specified	Uncertain significance (Jul 30, 2024)
3-169926757-G-T		not specified	Uncertain significance (Mar 01, 2025)
3-169926776-C-G		not specified	Uncertain significance (Sep 14, 2022)
3-169926780-T-G		not specified	Uncertain significance (May 28, 2024)
3-169926851-G-T		not specified	Uncertain significance (Jul 14, 2023)
3-169926861-G-A		not specified	Likely benign (Jan 20, 2025)
3-169926867-A-G		not specified	Uncertain significance (Jun 13, 2024)
3-169926912-C-T		not specified	Uncertain significance (Apr 05, 2023)
3-169927037-C-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAMD7	protein_coding	protein_coding	ENST00000428432	7	27604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000114	0.814	125707	0	40	125747	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.180	241	249	0.968	0.0000125	2922
Missense in Polyphen		45	44.084	1.0208		589
Synonymous	-0.0954	89	87.9	1.01	0.00000452	879
Loss of Function	1.39	12	18.4	0.651	9.79e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000336	0.000332
Ashkenazi Jewish	0.00	0.00
East Asian	0.000331	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000331	0.000326
South Asian	0.0000688	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the regulation of gene expression in the retina. It functions as a negative regulator of CRX-controlled genes. {ECO:0000250|UniProtKB:Q8C8Y5}.

Recessive Scores

• pRec: 0.0873

Intolerance Scores

• loftool: 0.719
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.394
• hipred: N
• hipred_score: 0.123
• ghis: 0.381

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0486

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Samd7
• Phenotype: vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: negative regulation of gene expression
• Cellular component: nucleus;cytoplasm