SPECC1

sperm antigen with calponin homology and coiled-coil domains 1

Basic information

Region (hg38): 17:20008864-20319026

Previous symbols: [ "CYTSB" ]

Links

ENSG00000128487 ∙ NCBI:92521 ∙ OMIM:608793 ∙ HGNC:30615 ∙ Uniprot:Q5M775 ∙ 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 SPECC1 gene.

• Inborn genetic diseases (45 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPECC1 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			43	3		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	4	0

Variants in SPECC1

This is a list of pathogenic ClinVar variants found in the SPECC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-20096698-G-T		not specified	Uncertain significance (Dec 16, 2023)
17-20096713-G-A		not specified	Uncertain significance (Aug 02, 2022)
17-20096733-G-C		not specified	Uncertain significance (Feb 10, 2022)
17-20096785-C-T		not specified	Uncertain significance (May 25, 2022)
17-20110556-G-A		not specified	Uncertain significance (Dec 11, 2023)
17-20110560-C-G		not specified	Uncertain significance (Dec 02, 2021)
17-20204344-A-T		not specified	Uncertain significance (Jul 20, 2021)
17-20204354-G-A		not specified	Uncertain significance (Mar 31, 2022)
17-20204417-G-A		not specified	Uncertain significance (May 30, 2023)
17-20204449-A-C		not specified	Uncertain significance (Dec 20, 2023)
17-20204470-C-T		not specified	Uncertain significance (Mar 22, 2022)
17-20204516-A-G		not specified	Uncertain significance (Sep 29, 2023)
17-20204550-G-C		not specified	Uncertain significance (Feb 05, 2024)
17-20204725-A-G		not specified	Uncertain significance (Dec 21, 2023)
17-20204759-A-T		Inborn genetic diseases	Uncertain significance (Jan 31, 2022)
17-20204773-G-C		not specified	Uncertain significance (Feb 06, 2024)
17-20204792-G-A		not specified	Likely benign (Nov 15, 2023)
17-20204815-T-G		not specified	Uncertain significance (Nov 13, 2023)
17-20204863-G-A		not specified	Uncertain significance (Jun 12, 2023)
17-20204910-C-G		not specified	Uncertain significance (Sep 06, 2022)
17-20204914-A-G		not specified	Likely benign (Jun 28, 2022)
17-20204930-C-G		not specified	Uncertain significance (Oct 05, 2023)
17-20204960-T-C		not specified	Likely benign (Dec 17, 2021)
17-20204999-G-A		not specified	Uncertain significance (Aug 11, 2022)
17-20205001-G-A		not specified	Uncertain significance (Jan 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPECC1	protein_coding	protein_coding	ENST00000261503	14	309683

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000868	0.999	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.188	619	606	1.02	0.0000351	6961
Missense in Polyphen		191	222.44	0.85864		2677
Synonymous	-1.70	270	237	1.14	0.0000138	2124
Loss of Function	4.23	14	44.4	0.315	0.00000228	561

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000593	0.000591
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000327	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000230	0.000229
Middle Eastern	0.000327	0.000326
South Asian	0.000425	0.000425
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0875

Intolerance Scores

• rvis_EVS: -1.19
• rvis_percentile_EVS: 5.89

Haploinsufficiency Scores

• pHI: 0.0963
• hipred: N
• hipred_score: 0.474
• ghis: 0.527

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: Specc1

Zebrafish Information Network

• Gene name: specc1
• Affected structure: hyosymplectic cartilage
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: actin cytoskeleton organization
• Cellular component: nucleus;microtubule organizing center;membrane;filamentous actin