SMR3A

submaxillary gland androgen regulated protein 3A

Basic information

Region (hg38): 4:70360760-70367158

Previous symbols: [ "PROL5" ]

Links

ENSG00000109208 ∙ NCBI:26952 ∙ OMIM:618340 ∙ HGNC:19216 ∙ Uniprot:Q99954 ∙ 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 SMR3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMR3A 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					1	1
missense			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	1

Variants in SMR3A

This is a list of pathogenic ClinVar variants found in the SMR3A region.

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

Position	Type	Phenotype	Significance	ClinVar
4-70362150-C-G		not specified	Uncertain significance (Dec 10, 2024)
4-70362159-C-G		not specified	Uncertain significance (Dec 12, 2023)
4-70366652-G-A			Benign (May 30, 2018)
4-70366652-G-C		not specified	Uncertain significance (Jul 10, 2023)
4-70366732-G-A		not specified	Uncertain significance (Nov 01, 2022)
4-70366771-G-A		not specified	Uncertain significance (Dec 17, 2021)
4-70366788-C-A		not specified	Uncertain significance (Oct 12, 2024)
4-70366792-C-A		not specified	Uncertain significance (May 09, 2023)
4-70366807-C-T		not specified	Uncertain significance (Apr 07, 2023)
4-70366809-G-A		not specified	Uncertain significance (Jan 23, 2023)
4-70366817-C-G		not specified	Uncertain significance (Sep 06, 2022)
4-70366854-A-G		not specified	Uncertain significance (Jan 23, 2024)
4-70366894-A-T		not specified	Uncertain significance (Feb 22, 2023)
4-70366915-C-A		not specified	Uncertain significance (Nov 06, 2023)
4-70366971-G-T		not specified	Uncertain significance (Mar 08, 2025)
4-70366981-C-T		not specified	Uncertain significance (May 23, 2023)
4-70366986-G-A		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMR3A	protein_coding	protein_coding	ENST00000226460	2	6398

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.391	0.484	125422	0	5	125427	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.590	84	70.1	1.20	0.00000307	817
Missense in Polyphen
Synonymous	0.751	20	24.8	0.808	0.00000106	323
Loss of Function	0.920	0	0.986	0.00	4.16e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000265	0.0000265
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in protection or detoxification. {ECO:0000250}.

Intolerance Scores

• loftool: 0.765
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.28

Haploinsufficiency Scores

• pHI: 0.151
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smr3a

Gene ontology

• Biological process: negative regulation of endopeptidase activity;regulation of sensory perception of pain
• Cellular component: extracellular region
• Molecular function: endopeptidase inhibitor activity