CCSER1

protein-coding

coiled-coil serine rich protein 1

Gene summary

Predicted to act upstream of or within several processes, including osteoclast differentiation; protein activation cascade; and protein stabilization. Implicated in alcohol dependence and cocaine dependence. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM190A

MANE transcript

NM_001145065.2

Inheritance

—

ClinVar variants

U:131B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.34

Max pathogenic AF

—

Genomic locus

chr4:90,127,394-91,605,295

External References & Databases

Ensembl (ENSG00000184305)

Transcript & Mutation Effects

hg38 • Region Span ~1,477.9 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 CCSER1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 129

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145065.2. 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	1 clinvar		2
missense			128 clinvar	4 clinvar	1 clinvar	133
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	131	5	1	137

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145065.2	RefSeq	NP_001138537.1	10	MANE Select
ENST00000509176.6	Ensembl	ENSP00000425040.1	10	MANE Select
NM_001377987.1	RefSeq	NP_001364916.1	9	Standard
NM_207491.2	RefSeq	NP_997374.1	7	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000509176
Coding exons: 10
Length: 1474379
Individuals with no LoFs: 124616
Homozygous LoFs: 0
Heterozygous LoFs: 20
Defined: 124636
p: 0.0000802

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.12	397	465	0.854	0.0000239	5857
Missense (PolyPhen)		127	168.89	0.75198		2310
Synonymous	0.286	170	175	0.973	0.00000944	1764
Loss of Function	3.64	12	35.4	0.339	0.00000196	471

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.000092	0.000087	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0.000038	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 0.82
RVIS percentile EVS: 88.07

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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