SLIRP

SRA stem-loop interacting RNA binding protein, the group of RNA binding motif containing

Basic information

Region (hg38): 14:77708071-77761104

Previous symbols: [ "C14orf156" ]

Links

ENSG00000119705 ∙ NCBI:81892 ∙ OMIM:610211 ∙ HGNC:20495 ∙ Uniprot:Q9GZT3 ∙ 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 SLIRP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLIRP 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			6			6
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding		1				1
Total	0	2	6	0	0

Variants in SLIRP

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

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

Position	Type	Phenotype	Significance	ClinVar
14-77708127-G-T		not specified	Uncertain significance (Apr 18, 2023)
14-77708169-G-C		not specified	Uncertain significance (Sep 06, 2022)
14-77710660-A-G		Mitochondrial encephalomyopathy	Likely pathogenic (Nov 25, 2020)
14-77710867-G-A		not specified	Uncertain significance (May 21, 2024)
14-77715827-A-G		not specified	Uncertain significance (Sep 01, 2021)
14-77715845-T-A		not specified	Uncertain significance (Sep 01, 2021)
14-77715859-CATATT-C		Mitochondrial encephalomyopathy	Likely pathogenic (Nov 25, 2020)
14-77715869-A-G		not specified	Uncertain significance (Sep 27, 2022)
14-77717551-A-G		not specified	Uncertain significance (Feb 12, 2024)
14-77718143-T-A		not specified	Uncertain significance (Sep 11, 2024)
14-77718251-C-T		not specified	Uncertain significance (Oct 02, 2023)
14-77718263-G-C		not specified	Uncertain significance (Mar 16, 2024)
14-77718439-A-G		not specified	Uncertain significance (Nov 22, 2023)
14-77718509-C-A		not specified	Uncertain significance (Jun 10, 2024)
14-77720751-T-C		not specified	Uncertain significance (May 17, 2023)
14-77720761-G-A		not specified	Uncertain significance (Dec 10, 2024)
14-77720805-T-C		not specified	Uncertain significance (Apr 01, 2022)
14-77723221-G-C		not specified	Uncertain significance (Jul 25, 2023)
14-77723262-C-T		not specified	Uncertain significance (May 06, 2024)
14-77731109-C-T		not specified	Uncertain significance (Jan 18, 2023)
14-77732501-T-C		not specified	Uncertain significance (Feb 27, 2024)
14-77732546-G-A		not specified	Uncertain significance (Apr 07, 2022)
14-77736990-T-C		not specified	Uncertain significance (May 21, 2024)
14-77737003-C-T		not specified	Uncertain significance (Aug 04, 2021)
14-77737025-C-A			Uncertain significance (Nov 01, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLIRP	protein_coding	protein_coding	ENST00000557342	4	53034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.73e-7	0.103	125695	0	51	125746	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.570	73	60.5	1.21	0.00000290	708
Missense in Polyphen		19	18.589	1.0221		258
Synonymous	-1.30	30	22.2	1.35	0.00000113	208
Loss of Function	-0.801	8	5.90	1.36	2.50e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00160	0.00160
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding protein that acts as a nuclear receptor corepressor. Probably acts by binding the SRA RNA, and repressing the SRA-mediated nuclear receptor coactivation. Binds the STR7 loop of SRA RNA. Also able to repress glucocorticoid (GR), androgen (AR), thyroid (TR) and VDR-mediated transactivation. {ECO:0000269|PubMed:16762838}.

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.0368
• hipred: N
• hipred_score: 0.461
• ghis: 0.505

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• 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: Slirp
• 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); reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of mitochondrial RNA catabolic process;spermatid development;single fertilization;flagellated sperm motility;mitochondrion morphogenesis
• Cellular component: acrosomal vesicle;nucleus;mitochondrion;sperm flagellum;perinuclear region of cytoplasm;ribonucleoprotein complex
• Molecular function: RNA binding;protein binding