SLF1

SMC5-SMC6 complex localization factor 1, the group of Ankyrin repeat domain containing

Basic information

Region (hg38): 5:94618668-94739436

Previous symbols: [ "BRCTD1", "ANKRD32" ]

Links

ENSG00000133302 ∙ NCBI:84250 ∙ OMIM:618467 ∙ HGNC:25408 ∙ Uniprot:Q9BQI6 ∙ 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 SLF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLF1 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	2	3
missense			60	3	1	64
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	60	4	3

Variants in SLF1

This is a list of pathogenic ClinVar variants found in the SLF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-94628821-G-A		not specified	Uncertain significance (Feb 23, 2023)
5-94628918-G-C		not specified	Uncertain significance (Jan 04, 2022)
5-94629103-T-C			Benign (Mar 29, 2018)
5-94629162-C-T		not specified	Uncertain significance (Apr 27, 2022)
5-94630530-T-C		not specified	Uncertain significance (Mar 25, 2024)
5-94630544-A-G		not specified	Uncertain significance (May 24, 2023)
5-94630647-G-C		not specified	Uncertain significance (Mar 15, 2024)
5-94630661-C-T		not specified	Uncertain significance (Sep 01, 2021)
5-94630741-A-G		not specified	Uncertain significance (Nov 03, 2023)
5-94643278-T-C		not specified	Uncertain significance (Jun 21, 2021)
5-94643279-G-T		not specified	Uncertain significance (Apr 07, 2022)
5-94643298-G-C		not specified	Uncertain significance (Oct 12, 2022)
5-94643343-G-T		not specified	Uncertain significance (Aug 13, 2021)
5-94643344-C-T		not specified	Uncertain significance (Aug 13, 2021)
5-94649488-A-G		not specified	Likely benign (Jul 13, 2021)
5-94649552-T-G		not specified	Uncertain significance (May 22, 2024)
5-94649596-A-G			Likely benign (Oct 01, 2022)
5-94651741-A-G		not specified	Likely benign (Apr 20, 2024)
5-94651768-A-G		not specified	Uncertain significance (Jul 26, 2022)
5-94651785-T-G		not specified	Uncertain significance (Aug 04, 2023)
5-94651808-T-G		not specified	Uncertain significance (May 08, 2023)
5-94651817-C-A		not specified	Uncertain significance (Jan 24, 2023)
5-94651835-A-G		not specified	Uncertain significance (Aug 16, 2021)
5-94653291-A-G		not specified	Uncertain significance (Nov 07, 2022)
5-94653344-G-C		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLF1	protein_coding	protein_coding	ENST00000265140	20	121090

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.85e-10	1.00	125701	0	47	125748	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.453	446	474	0.941	0.0000226	6978
Missense in Polyphen		95	147.35	0.64471		2092
Synonymous	0.101	163	165	0.990	0.00000804	1893
Loss of Function	3.15	23	46.1	0.499	0.00000217	728

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000405	0.000402
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000109
Finnish	0.0000929	0.0000924
European (Non-Finnish)	0.000266	0.000264
Middle Eastern	0.000114	0.000109
South Asian	0.0000995	0.0000980
Other	0.000334	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the DNA damage response (DDR) pathway by regulating postreplication repair of UV-damaged DNA and genomic stability maintenance (PubMed:25931565). The SLF1-SLF2 complex acts to link RAD18 with the SMC5-SMC6 complex at replication- coupled interstrand cross-links (ICL) and DNA double-strand breaks (DSBs) sites on chromatin during DNA repair in response to stalled replication forks (PubMed:25931565). Promotes the recruitment of SLF2 and the SMC5-SMC6 complex to DNA lesions (PubMed:25931565). {ECO:0000269|PubMed:25931565}.

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.169
• ghis: 0.599

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Slf1
• Phenotype: normal phenotype

Gene ontology

• Biological process: DNA repair;cellular response to DNA damage stimulus;positive regulation of protein complex assembly;positive regulation of maintenance of mitotic sister chromatid cohesion;protein localization to site of double-strand break;positive regulation of double-strand break repair
• Cellular component: nucleosome;nucleus;cytoplasm;centrosome;site of double-strand break;nuclear inclusion body
• Molecular function: protein binding;ubiquitin protein ligase binding;protein-containing complex binding