POC1B

POC1 centriolar protein B, the group of WD repeat domain containing

Basic information

Region (hg38): 12:89419717-89526047

Previous symbols: [ "WDR51B" ]

Links

ENSG00000139323 ∙ NCBI:282809 ∙ OMIM:614784 ∙ HGNC:30836 ∙ Uniprot:Q8TC44 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cone-rod dystrophy 20 (Strong), mode of inheritance: AR
• cone-rod dystrophy (Supportive), mode of inheritance: AD
• cone-rod dystrophy 20 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cone-rod dystrophy 20	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	24945461; 25018096

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POC1B gene.

• not provided (311 variants)
• Inborn genetic diseases (23 variants)
• Cone-rod dystrophy 20 (12 variants)
• Retinal dystrophy (2 variants)
• Childhood-onset schizophrenia (1 variants)
• Cone-rod dystrophy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POC1B 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				42	4	46
missense	2		141	9	2	154
nonsense	4	3	1			8
start loss			1			1
frameshift	11	1				12
inframe indel						0
splice donor/acceptor (+/-2bp)	4	4				8
splice region	1		5	9	2	17
non coding	1	1	7	54	16	79
Total	22	9	150	105	22

Highest pathogenic variant AF is 0.0000527

Variants in POC1B

This is a list of pathogenic ClinVar variants found in the POC1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-89421157-C-A		POC1B-related disorder	Benign (Jan 25, 2024)
12-89421159-T-G			Uncertain significance (Nov 15, 2022)
12-89421165-T-G			Uncertain significance (Feb 19, 2021)
12-89421171-A-G			Likely benign (Aug 16, 2022)
12-89421176-T-G			Uncertain significance (May 25, 2022)
12-89421181-A-G			Uncertain significance (Jan 16, 2022)
12-89421192-A-G			Likely benign (Aug 22, 2022)
12-89421224-T-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2022)
12-89421225-C-T			Likely benign (Nov 03, 2023)
12-89421232-A-T		Inborn genetic diseases	Uncertain significance (Mar 01, 2022)
12-89421235-C-T			Uncertain significance (Oct 11, 2021)
12-89421240-C-T			Likely benign (May 22, 2021)
12-89421264-A-G			Likely benign (Dec 11, 2023)
12-89425141-G-A			Likely benign (Apr 24, 2021)
12-89425148-G-C			Likely benign (Nov 08, 2022)
12-89425156-C-T		Cone-rod dystrophy 20	Conflicting classifications of pathogenicity (Nov 06, 2023)
12-89425160-C-CCT		Cone-rod dystrophy 20	Pathogenic/Likely pathogenic (Jul 28, 2022)
12-89425162-T-C			Uncertain significance (May 01, 2017)
12-89425177-A-G			Uncertain significance (May 01, 2017)
12-89425181-G-A			Pathogenic (Sep 06, 2022)
12-89425193-G-C			Uncertain significance (Jul 14, 2022)
12-89425198-A-T			Pathogenic (Jul 14, 2023)
12-89425203-A-C			Uncertain significance (Jul 17, 2022)
12-89425208-T-C			Uncertain significance (Jul 26, 2022)
12-89425214-C-A			Uncertain significance (Sep 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POC1B	protein_coding	protein_coding	ENST00000313546	12	106307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.05e-8	0.923	125694	0	54	125748	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0928	254	250	1.02	0.0000122	3107
Missense in Polyphen		82	95.44	0.85918		1213
Synonymous	1.21	76	90.7	0.838	0.00000473	906
Loss of Function	1.82	16	26.0	0.614	0.00000140	326

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000204	0.000204
Ashkenazi Jewish	0.00	0.00
East Asian	0.000796	0.000761
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000210	0.000202
Middle Eastern	0.000796	0.000761
South Asian	0.000261	0.000229
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in centriole assembly and/or stability and ciliogenesis (PubMed:20008567). Involved in early steps of centriole duplication, as well as in the later steps of centriole length control (PubMed:19109428). Acts in concert with POC1A to ensure centriole integrity and proper mitotic spindle formation. Required for primary cilia formation, ciliary length and also cell proliferation (PubMed:23015594). Required for retinal integrity (PubMed:25044745). {ECO:0000269|PubMed:19109428, ECO:0000269|PubMed:20008567, ECO:0000269|PubMed:23015594, ECO:0000269|PubMed:25044745}.
• Disease: DISEASE: Cone-rod dystrophy 20 (CORD20) [MIM:615973]: A form of cone-rod dystrophy, an inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa, due to cone photoreceptors degenerating at a higher rate than rod photoreceptors. {ECO:0000269|PubMed:24945461, ECO:0000269|PubMed:25018096, ECO:0000269|PubMed:25044745}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.333
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Poc1b

Zebrafish Information Network

• Gene name: poc1b
• Affected structure: retinal cone cell
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: retina homeostasis;cell population proliferation;cilium assembly
• Cellular component: spindle pole;centrosome;centriole;ciliary basal body
• Molecular function: protein binding