TBC1D31

protein-coding

TBC1 domain family member 31, the group of WD repeat domain containing

Gene summary

Enables molecular adaptor activity. Involved in cilium assembly. Located in centriolar satellite and ciliary basal body. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

WDR67

MANE transcript

NM_145647.4

Inheritance

ClinVar variants

P:1U:171B:15

Top phenotype

TBC1D31-related disorder

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr8:123,041,968-123,152,153

External References & Databases

Ensembl (ENSG00000156787)

Transcript & Mutation Effects

hg38 • Region Span ~110.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

congenital anomaly of kidney and urinary tractLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0019719

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TBC1D31 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 161

TBC1D31-related disorderTotal: 10

not providedTotal: 4

Inherited genitourinary tract anomaliesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145647.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense		1 clinvar	152 clinvar	14 clinvar		167
nonsense			1 clinvar			1
start loss						0
frameshift			7 clinvar			7
splice donor/acceptor (+/-2bp)			8 clinvar			8
Total	0	1	171	15	0	187

Highest pathogenic variant AF is 0.00035294087

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145647.4	RefSeq	NP_663622.2	22	MANE Select
ENST00000287380.6	Ensembl	ENSP00000287380.1	22	MANE Select
NM_001145088.2	RefSeq	NP_001138560.1	20	Standard
NM_001330606.2	RefSeq	NP_001317535.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

centrosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000287380
Coding exons: 22
Length: 110186
Individuals with no LoFs: 125581
Homozygous LoFs: 0
Heterozygous LoFs: 166
Defined: 125747
p: 0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.906	486	546	0.891	0.0000272	7063
Missense (PolyPhen)		88	116.91	0.75273		1524
Synonymous	1.14	168	188	0.894	0.00000927	1916
Loss of Function	2.47	40	60.7	0.659	0.00000334	703

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0014	notable
Latino/Admixed American	0.00089	0.00087	rare
Ashkenazi Jewish	0.00060	0.00060	rare
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00072	0.00070	rare
South Asian	0.00053	0.00052	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0998

Intolerance Scores

RVIS EVS: 0.1
RVIS percentile EVS: 60.76

Essentials

Essential (CRISPR): N
Essential (gene trap): H

Gene Damage Prediction

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