POC1A

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

Basic information

Region (hg38): 3:52075226-52154690

Previous symbols: [ "WDR51A" ]

Links

ENSG00000164087 ∙ NCBI:25886 ∙ OMIM:614783 ∙ HGNC:24488 ∙ Uniprot:Q8NBT0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Fanconi anemia complementation group Q (Definitive), mode of inheritance: AR
• short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome (Supportive), mode of inheritance: AR
• short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis (SOFT syndrome)	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	Craniofacial; Dental; Dermatologic; Endocrine; Genitourinary; Musculoskeletal; Neurologic	22840363; 22840364; 22440536

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the POC1A gene.

• not provided (5 variants)
• Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome (3 variants)
• Ateleiotic dwarfism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the POC1A 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				33	3	36
missense		2	53	4	2	61
nonsense	2	1				3
start loss	2					2
frameshift	3		1			4
inframe indel			1			1
splice donor/acceptor (+/-2bp)		3				3
splice region			2	10	1	13
non coding				21	9	30
Total	7	6	55	58	14

Highest pathogenic variant AF is 0.00000657

Variants in POC1A

This is a list of pathogenic ClinVar variants found in the POC1A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-52075652-C-T			Benign (Jun 20, 2021)
3-52075825-T-C			Benign (Nov 12, 2018)
3-52075889-A-G			Uncertain significance (Oct 04, 2022)
3-52075941-C-T			Likely benign (Feb 19, 2022)
3-52075962-C-A			Likely benign (Jun 18, 2022)
3-52075981-ACTGT-A		not specified	Uncertain significance (Jun 27, 2023)
3-52096585-A-G			Uncertain significance (Nov 28, 2022)
3-52096608-C-T			Likely benign (Jan 22, 2024)
3-52096609-G-A		Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome	Uncertain significance (Oct 18, 2022)
3-52096637-C-T		Inborn genetic diseases	Uncertain significance (Jun 13, 2024)
3-52096645-TG-T		POC1A-related syndrome	Pathogenic (Sep 19, 2020)
3-52096650-C-A		not specified	Benign (Jan 29, 2024)
3-52096659-C-T			Likely benign (Oct 05, 2022)
3-52096672-C-A		Inborn genetic diseases	Uncertain significance (Mar 26, 2024)
3-52096688-G-C			Uncertain significance (May 09, 2023)
3-52096689-G-A			Likely benign (Oct 19, 2022)
3-52096701-G-A			Likely benign (Oct 07, 2023)
3-52096710-T-C			Likely benign (Aug 15, 2022)
3-52096717-AG-A			Likely benign (Oct 03, 2022)
3-52096720-C-A			Likely benign (Jul 17, 2017)
3-52096722-G-A			Likely benign (Jul 17, 2017)
3-52096732-A-C			Likely benign (Jan 12, 2024)
3-52096732-A-G			Likely benign (May 09, 2023)
3-52122378-C-T		Short stature-onychodysplasia-facial dysmorphism-hypotrichosis syndrome	Pathogenic (Aug 05, 2021)
3-52122380-A-G			Uncertain significance (Aug 16, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
POC1A	protein_coding	protein_coding	ENST00000296484	11	79438

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000330	0.942	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.08	201	249	0.808	0.0000149	2654
Missense in Polyphen		79	102.02	0.77437		1031
Synonymous	0.673	93	102	0.915	0.00000660	810
Loss of Function	1.80	12	20.9	0.575	0.00000106	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000167	0.000167
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays an important role in centriole assembly and/or stability and ciliogenesis. Involved in early steps of centriole duplication, as well as in the later steps of centriole length control. Acts in concert with POC1B to ensure centriole integrity and proper mitotic spindle formation. {ECO:0000269|PubMed:19109428, ECO:0000269|PubMed:23015594}.
• Disease: DISEASE: Short stature, onychodysplasia, facial dysmorphism, and hypotrichosis (SOFT) [MIM:614813]: A syndrome characterized by severely short long bones, peculiar facies associated with paucity of hair, and nail anomalies. Growth retardation is evident on prenatal ultrasound as early as the second trimester of pregnancy, and affected individuals reach a final stature consistent with a height age of 6 years to 8 years. Relative macrocephaly is present during early childhood but head circumference is markedly low by adulthood. Psychomotor development is normal. Facial dysmorphism includes a long, triangular face with prominent nose and small ears, and affected individuals have an unusual high-pitched voice. Clinodactyly, brachydactyly, and hypoplastic distal phalanges and fingernails are present in association with postpubertal sparse and short hair. Typical skeletal findings include short and thick long bones with mild irregular metaphyseal changes, short femoral necks, and hypoplastic pelvis and sacrum. All long bones of the hand are short, with major delay of carpal ossification and cone- shaped epiphyses. Vertebral body ossification is also delayed. {ECO:0000269|PubMed:22840363, ECO:0000269|PubMed:22840364}. Note=The disease is caused by mutations affecting the gene represented in this entry. Cells derived from affected individuals have abnormal mitotic mechanics with multipolar spindles, in addition to clearly impaired ciliogenesis.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.59

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.408
• ghis: 0.553

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Poc1a
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); reproductive system 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); skeleton phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: growth plate cartilage chondrocyte development;mitotic spindle organization;spermatogenesis;positive regulation of centrosome duplication;non-motile cilium assembly
• Cellular component: spindle pole;centrosome;centriole;ciliary basal body
• Molecular function: protein binding