SRBD1

S1 RNA binding domain 1

Basic information

Region (hg38): 2:45388680-45612165

Links

ENSG00000068784 ∙ NCBI:55133 ∙ ∙ HGNC:25521 ∙ Uniprot:Q8N5C6 ∙ 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 SRBD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRBD1 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			64	3		67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	3	0

Variants in SRBD1

This is a list of pathogenic ClinVar variants found in the SRBD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-45389443-G-C		not specified	Uncertain significance (Jun 17, 2024)
2-45389525-T-C		not specified	Uncertain significance (May 13, 2024)
2-45389545-A-G		not specified	Uncertain significance (Aug 15, 2023)
2-45392973-G-C		not specified	Uncertain significance (Dec 27, 2023)
2-45393022-C-G		not specified	Uncertain significance (Jan 08, 2024)
2-45393041-T-C		not specified	Uncertain significance (Apr 04, 2024)
2-45393067-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-45393100-T-C		not specified	Likely benign (Oct 12, 2021)
2-45393116-T-C		not specified	Uncertain significance (Jul 20, 2021)
2-45413118-T-C		not specified	Uncertain significance (Apr 05, 2023)
2-45413138-G-A		not specified	Uncertain significance (Mar 01, 2024)
2-45413163-G-C			Likely benign (Dec 01, 2022)
2-45413166-T-G		not specified	Uncertain significance (Jul 12, 2023)
2-45413183-T-G		not specified	Uncertain significance (Mar 29, 2024)
2-45413256-C-T		not specified	Uncertain significance (Oct 05, 2022)
2-45413289-G-C		not specified	Uncertain significance (Dec 16, 2023)
2-45418378-G-C		not specified	Uncertain significance (Jun 29, 2023)
2-45418432-G-C		not specified	Uncertain significance (Jan 26, 2022)
2-45418518-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-45418539-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-45477060-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-45477061-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-45477064-T-C		not specified	Uncertain significance (Nov 13, 2023)
2-45488246-T-C		not specified	Uncertain significance (Jun 07, 2023)
2-45488273-T-A		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRBD1	protein_coding	protein_coding	ENST00000263736	20	223486

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.69e-20	0.259	125625	0	123	125748	0.000489

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.85	638	519	1.23	0.0000266	6511
Missense in Polyphen		148	175.15	0.845		2194
Synonymous	-3.86	252	185	1.36	0.00000938	1888
Loss of Function	1.69	38	51.0	0.745	0.00000272	643

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000475	0.000474
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000490	0.000489
Finnish	0.000420	0.000416
European (Non-Finnish)	0.000675	0.000659
Middle Eastern	0.000490	0.000489
South Asian	0.000333	0.000327
Other	0.00102	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.19

Haploinsufficiency Scores

• pHI: 0.188
• hipred: N
• hipred_score: 0.333
• ghis: 0.495

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srbd1

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;translation
• Molecular function: mRNA binding;structural constituent of ribosome