FAM135A

protein-coding

family with sequence similarity 135 member A

Gene summary

Predicted to be involved in lipid metabolic process. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

KIAA1411

MANE transcript

NM_001162529.3

Inheritance

—

ClinVar variants

U:176B:6

Top phenotype

Histiocytoid cardiomyopathy

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr6:70,412,941-70,561,174

External References & Databases

Ensembl (ENSG00000082269)

Transcript & Mutation Effects

hg38 • Region Span ~148.2 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 FAM135A variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 166

not providedTotal: 4

Histiocytoid cardiomyopathyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001162529.3. 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	2 clinvar		4
missense			168 clinvar	3 clinvar		171
nonsense			2 clinvar	1 clinvar		3
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	176	6	0	182

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 130 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001162529.3	RefSeq	NP_001156001.1	19	MANE Select
ENST00000418814.7	Ensembl	ENSP00000410768.2	19	MANE Select
NM_001105531.3	RefSeq	NP_001099001.1	19	Standard
NM_001330995.3	RefSeq	NP_001317924.1	20	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular lipid metabolic process

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000418814
Coding exons: 19
Length: 148234
Individuals with no LoFs: 125714
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125726
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.33	639	741	0.862	0.0000355	10002
Missense (PolyPhen)		196	278.47	0.70386		3667
Synonymous	-0.274	270	264	1.02	0.0000131	2821
Loss of Function	6.25	10	63.9	0.156	0.00000352	865

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000064	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0900

Intolerance Scores

LoFtool: 0.635
RVIS EVS: -0.5
RVIS percentile EVS: 21.84

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.473

Gene Damage Prediction

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