SWSAP1

SWIM-type zinc finger 7 associated protein 1, the group of CTLH complex

Basic information

Region (hg38): 19:11374666-11376951

Previous symbols: [ "C19orf39" ]

Links

ENSG00000173928 ∙ NCBI:126074 ∙ OMIM:614536 ∙ HGNC:26638 ∙ Uniprot:Q6NVH7 ∙ 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 SWSAP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SWSAP1 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	2	0

Variants in SWSAP1

This is a list of pathogenic ClinVar variants found in the SWSAP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-11374771-C-G		not specified	Uncertain significance (Jul 12, 2022)
19-11374787-G-T		not specified	Uncertain significance (Nov 22, 2022)
19-11374799-C-T		not specified	Uncertain significance (Mar 06, 2025)
19-11374834-G-C		not specified	Uncertain significance (Dec 14, 2024)
19-11374845-A-C		not specified	Uncertain significance (May 23, 2023)
19-11374868-G-A		not specified	Uncertain significance (May 24, 2024)
19-11374893-C-G			Likely benign (Mar 01, 2025)
19-11374910-T-C		not specified	Uncertain significance (Mar 03, 2025)
19-11374916-C-A		not specified	Uncertain significance (Aug 26, 2024)
19-11375513-A-C		not specified	Uncertain significance (Dec 31, 2024)
19-11375535-C-T		not specified	Uncertain significance (Oct 08, 2024)
19-11375554-C-A		not specified	Likely benign (Nov 07, 2024)
19-11375576-G-A		not specified	Uncertain significance (Nov 16, 2022)
19-11375600-C-G		not specified	Uncertain significance (Nov 21, 2024)
19-11375612-G-C		not specified	Uncertain significance (Sep 06, 2024)
19-11375688-C-A		not specified	Uncertain significance (Apr 20, 2024)
19-11375707-C-A		not specified	Uncertain significance (Apr 08, 2022)
19-11375718-C-A		not specified	Uncertain significance (Mar 28, 2024)
19-11375773-T-G		not specified	Uncertain significance (Mar 31, 2024)
19-11375777-G-A		not specified	Uncertain significance (Oct 22, 2024)
19-11375867-C-G		not specified	Uncertain significance (Jun 24, 2022)
19-11375948-G-A		not specified	Likely benign (Jul 12, 2023)
19-11375967-C-G		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SWSAP1	protein_coding	protein_coding	ENST00000312423	2	2267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00422	0.678	125703	0	43	125746	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.319	144	134	1.08	0.00000690	1414
Missense in Polyphen		39	38.879	1.0031		463
Synonymous	0.377	57	60.7	0.938	0.00000319	545
Loss of Function	0.630	4	5.61	0.713	3.02e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000413	0.000412
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: ATPase which is preferentially stimulated by single- stranded DNA and is involved in homologous recombination repair (HRR). Has a DNA-binding activity which is independent of its ATPase activity. {ECO:0000269|PubMed:21965664}.

Intolerance Scores

• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.23

Haploinsufficiency Scores

• pHI: 0.144
• hipred: N
• hipred_score: 0.146
• ghis: 0.416

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: Swsap1

Gene ontology

• Biological process: double-strand break repair via homologous recombination;protein stabilization
• Cellular component: nucleus;Shu complex
• Molecular function: single-stranded DNA binding;protein binding;ATPase activity