FHIP1A

protein-coding

FHF complex subunit HOOK interacting protein 1A, the group of FHF complex

Gene summary

Involved in protein localization to perinuclear region of cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM160A1

MANE transcript

NM_001109977.3

Inheritance

—

ClinVar variants

U:169B:11

Top phenotype

High myopia

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr4:151,409,176-151,670,503

External References & Databases

Ensembl (ENSG00000164142)

Transcript & Mutation Effects

hg38 • Region Span ~261.3 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 FHIP1A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 173

not providedTotal: 3

High myopiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001109977.3. 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				2 clinvar	1 clinvar	3
missense			169 clinvar	8 clinvar		177
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	169	10	1	180

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001109977.3	RefSeq	NP_001103447.1	11	MANE Select
ENST00000435205.6	Ensembl	ENSP00000413196.1	11	MANE Select
NM_001348694.2	RefSeq	NP_001335623.1	11	Standard
ENST00000503146.5	Ensembl	ENSP00000424175.1	2	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000435205
Coding exons: 11
Length: 254417
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.30	403	556	0.725	0.0000292	6826
Missense (PolyPhen)		207	275.69	0.75085		3481
Synonymous	2.53	179	227	0.787	0.0000133	2041
Loss of Function	3.37	15	37.2	0.403	0.00000179	474

Population LoF Frequency

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

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1.98
RVIS percentile EVS: 97.61

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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