SH3D21

SH3 domain containing 21

Basic information

Region (hg38): 1:36306368-36329340

Previous symbols: [ "C1orf113" ]

Links

ENSG00000214193 ∙ NCBI:79729 ∙ ∙ HGNC:26236 ∙ Uniprot:A4FU49 ∙ 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 SH3D21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3D21 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		2
missense			42	5		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	2		12
Total	0	0	52	9	0

Variants in SH3D21

This is a list of pathogenic ClinVar variants found in the SH3D21 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36306598-A-T		not specified	Uncertain significance (Jan 29, 2024)
1-36306705-C-G		not specified	Uncertain significance (Mar 02, 2023)
1-36306711-G-A		not specified	Uncertain significance (Mar 29, 2023)
1-36306750-G-A		not specified	Uncertain significance (Jan 18, 2023)
1-36306857-C-G		not specified	Uncertain significance (Nov 29, 2021)
1-36306861-G-T		not specified	Uncertain significance (Aug 12, 2021)
1-36307181-C-A		not specified	Uncertain significance (Oct 18, 2021)
1-36307185-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-36307526-G-A		not specified	Uncertain significance (Jun 03, 2024)
1-36307770-G-T		not specified	Uncertain significance (Mar 31, 2024)
1-36307814-C-T		not specified	Uncertain significance (Mar 20, 2023)
1-36307818-C-T		not specified	Uncertain significance (May 05, 2023)
1-36307943-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-36308177-C-T		not specified	Uncertain significance (Oct 12, 2022)
1-36308182-G-C		not specified	Uncertain significance (Oct 26, 2021)
1-36308183-G-C		not specified	Uncertain significance (Oct 18, 2021)
1-36309567-G-A		not specified	Uncertain significance (Apr 26, 2024)
1-36319114-C-G			Likely benign (Jan 01, 2023)
1-36319136-A-G		not specified	Uncertain significance (Sep 22, 2023)
1-36319268-G-C		not specified	Uncertain significance (Sep 06, 2022)
1-36319304-G-A		not specified	Likely benign (May 28, 2024)
1-36319306-G-A		not specified	Uncertain significance (Feb 07, 2023)
1-36319448-A-G		not specified	Likely benign (Dec 20, 2021)
1-36319506-G-C		not specified	Uncertain significance (Jun 07, 2024)
1-36319510-C-T		not specified	Likely benign (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3D21	protein_coding	protein_coding	ENST00000453908	16	18497

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.79e-12	0.884	121128	0	3	121131	0.0000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.585	383	417	0.919	0.0000216	4818
Missense in Polyphen		91	104.8	0.86829		1379
Synonymous	1.17	157	177	0.888	0.00000981	1555
Loss of Function	1.91	23	35.2	0.653	0.00000185	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000166
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000166	0.000166
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• pHI: 0.0336
• hipred: N
• hipred_score: 0.123
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: Sh3d21

Gene ontology

• Cellular component: nucleus;nucleoplasm;plasma membrane