FHDC1

protein-coding

FH2 domain containing 1, the group of Formins

Gene summary

Predicted to enable actin binding activity and microtubule binding activity. Involved in Golgi ribbon formation; cilium assembly; and stress fiber assembly. Located in cilium and microtubule. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001371116.1

Inheritance

—

ClinVar variants

U:200B:20

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.37

Max pathogenic AF

—

Genomic locus

chr4:152,936,323-152,979,671

External References & Databases

Ensembl (ENSG00000137460)

Transcript & Mutation Effects

hg38 • Region Span ~43.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FHDC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 206

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001371116.1. 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			1 clinvar	2 clinvar	4 clinvar	7
missense			196 clinvar	10 clinvar	4 clinvar	210
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	200	12	8	220

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001371116.1	RefSeq	NP_001358045.1	11	MANE Select
ENST00000511601.6	Ensembl	ENSP00000427567.1	11	MANE Select
NM_033393.3	RefSeq	NP_203751.2	11	Standard
ENST00000876678.1	Ensembl	ENSP00000546737.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

stress fiber assembly
cilium assembly
Golgi ribbon formation

Molecular Function

actin binding
microtubule binding

Cellular Component

Golgi apparatus
microtubule
cytoplasmic microtubule
cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000511601
Coding exons: 11
Length: 43345
Individuals with no LoFs: 125719
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125748
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.110	659	667	0.988	0.0000397	7346
Missense (PolyPhen)		156	182.57	0.85447		2170
Synonymous	-0.0337	275	274	1.00	0.0000168	2392
Loss of Function	3.55	14	37.4	0.374	0.00000198	464

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00014	0.00013	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Microtubule-associated formin which regulates both actin and microtubule dynamics. Induces microtubule acetylation and stabilization and actin stress fiber formation (PubMed:18815276). Regulates Golgi ribbon formation (PubMed:26564798). Required for normal cilia assembly. Early in cilia assembly, may assist in the maturation and positioning of the centrosome/basal body, and once cilia assembly has initiated, may also promote cilia elongation by inhibiting disassembly (PubMed:29742020). {ECO:0000269|PubMed:18815276, ECO:0000269|PubMed:26564798, ECO:0000269|PubMed:29742020}.;

Recessive Scores

pRec: 0.0895

Intolerance Scores

LoFtool: 0.662
RVIS EVS: 0.97
RVIS percentile EVS: 90.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0778

Gene Damage Prediction

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