PABIR3

PABIR family member 3

Basic information

Region (hg38): X:134796395-134854835

Previous symbols: [ "FAM122C" ]

Links

ENSG00000156500 ∙ NCBI:159091 ∙ ∙ HGNC:25202 ∙ Uniprot:Q6P4D5 ∙ 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 PABIR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PABIR3 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			10	1		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	10	2	0

Variants in PABIR3

This is a list of pathogenic ClinVar variants found in the PABIR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-134807614-A-G		not specified	Uncertain significance (Oct 07, 2024)
X-134807618-A-T		not specified	Uncertain significance (Nov 30, 2021)
X-134807653-G-A		not specified	Likely benign (Jun 28, 2023)
X-134807658-C-A		not specified	Uncertain significance (May 05, 2023)
X-134814841-C-T		not specified	Uncertain significance (Sep 12, 2024)
X-134821550-G-A			Likely benign (Dec 01, 2022)
X-134829254-C-G		not specified	Uncertain significance (Dec 17, 2024)
X-134829262-C-T		not specified	Uncertain significance (Jul 13, 2021)
X-134845226-A-G		not specified	Uncertain significance (Jan 17, 2025)
X-134845384-G-A		not specified	Uncertain significance (Nov 20, 2024)
X-134847462-A-G			Likely benign (-)
X-134852821-A-G		not specified	Conflicting classifications of pathogenicity (Mar 01, 2023)
X-134852859-T-G		not specified	Uncertain significance (Dec 27, 2022)
X-134852893-T-C		not specified	Conflicting classifications of pathogenicity (Nov 25, 2024)
X-134854118-C-T		not specified	Uncertain significance (Jan 15, 2025)
X-134854135-C-A		not specified	Uncertain significance (May 25, 2022)
X-134854160-C-T		not specified	Uncertain significance (May 10, 2024)
X-134854197-A-G		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PABIR3	protein_coding	protein_coding	ENST00000370784	7	57822

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000209	0.510	123961	6	0	123967	0.0000242

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0534	67	65.8	1.02	0.00000479	1281
Missense in Polyphen		12	12.333	0.97298		200
Synonymous	-0.0636	23	22.6	1.02	0.00000158	361
Loss of Function	0.398	6	7.15	0.839	5.04e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000735	0.0000547
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000735	0.0000547
South Asian	0.000299	0.000173
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.546
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.0622
• hipred: N
• hipred_score: 0.145
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00101

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam122c
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype