SSRP1

structure specific recognition protein 1

Basic information

Region (hg38): 11:57325986-57335892

Links

ENSG00000149136 ∙ NCBI:6749 ∙ OMIM:604328 ∙ HGNC:11327 ∙ Uniprot:Q08945 ∙ 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 SSRP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSRP1 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					3	3
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	3

Variants in SSRP1

This is a list of pathogenic ClinVar variants found in the SSRP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57326460-G-C		not specified	Uncertain significance (Jul 12, 2022)
11-57326463-C-G		not specified	Uncertain significance (Dec 06, 2022)
11-57326467-T-C			Benign (May 21, 2018)
11-57326708-T-C		not specified	Uncertain significance (Aug 28, 2024)
11-57326753-C-T		not specified	Uncertain significance (Jun 10, 2024)
11-57326834-G-T		not specified	Uncertain significance (Mar 20, 2023)
11-57326836-G-A		not specified	Uncertain significance (Jan 16, 2025)
11-57326836-G-C		not specified	Uncertain significance (Feb 27, 2025)
11-57326852-T-C		not specified	Uncertain significance (Apr 01, 2024)
11-57327499-C-T		not specified	Uncertain significance (Mar 11, 2025)
11-57327505-G-A		not specified	Uncertain significance (May 26, 2024)
11-57327743-A-C		not specified	Uncertain significance (Jul 16, 2024)
11-57327768-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-57327803-T-A		not specified	Uncertain significance (May 03, 2023)
11-57327860-T-C		not specified	Uncertain significance (Aug 14, 2024)
11-57328359-G-A		not specified	Uncertain significance (Mar 11, 2025)
11-57332227-G-A		not specified	Uncertain significance (Jan 24, 2024)
11-57332239-T-C		not specified	Uncertain significance (Feb 05, 2025)
11-57332786-G-A		not specified	Uncertain significance (Nov 21, 2022)
11-57332997-C-T		not specified	Uncertain significance (Sep 27, 2021)
11-57332998-G-A			Benign (Dec 31, 2019)
11-57333030-C-T		not specified	Uncertain significance (May 09, 2023)
11-57333486-C-T		not specified	Uncertain significance (Dec 07, 2024)
11-57333500-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-57333501-G-A		not specified	Uncertain significance (Apr 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SSRP1	protein_coding	protein_coding	ENST00000278412	16	9893

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00415	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.04	189	423	0.447	0.0000251	4730
Missense in Polyphen		24	107.16	0.22396		1271
Synonymous	1.25	134	154	0.872	0.00000906	1281
Loss of Function	4.98	5	38.3	0.131	0.00000204	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II. The FACT complex is probably also involved in phosphorylation of 'Ser-392' of p53/TP53 via its association with CK2 (casein kinase II). Binds specifically to double-stranded DNA and at low levels to DNA modified by the antitumor agent cisplatin. May potentiate cisplatin-induced cell death by blocking replication and repair of modified DNA. Also acts as a transcriptional coactivator for p63/TP63. {ECO:0000269|PubMed:10912001, ECO:0000269|PubMed:11239457, ECO:0000269|PubMed:12374749, ECO:0000269|PubMed:12934006, ECO:0000269|PubMed:16713563, ECO:0000269|PubMed:9489704, ECO:0000269|PubMed:9566881, ECO:0000269|PubMed:9836642}.
• Pathway: Disease;Gene expression (Transcription);Formation of HIV-1 elongation complex containing HIV-1 Tat;Tat-mediated elongation of the HIV-1 transcript;HIV Transcription Elongation;HIV elongation arrest and recovery;Formation of HIV elongation complex in the absence of HIV Tat;Pausing and recovery of HIV elongation;Generic Transcription Pathway;Tat-mediated HIV elongation arrest and recovery;Pausing and recovery of Tat-mediated HIV elongation;Transcription of the HIV genome;Late Phase of HIV Life Cycle;HIV Life Cycle;HIV Infection;RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;Infectious disease;RNA Polymerase II Transcription Elongation;TP53 Regulates Transcription of DNA Repair Genes;Validated transcriptional targets of TAp63 isoforms;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.193

Intolerance Scores

• loftool: 0.0641
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.45

Haploinsufficiency Scores

• pHI: 0.783
• hipred: Y
• hipred_score: 0.825
• ghis: 0.699

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.846

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ssrp1
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: ssrp1a
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: DNA replication;DNA repair;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;regulation of signal transduction by p53 class mediator
• Cellular component: nucleoplasm;chromosome;nucleolus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;RNA binding;protein binding