Is CPLANE1 p.Ser3082Thr (c.9244T>A) pathogenic?

CPLANE1 p.Ser3082Thr (c.9244T>A) is classified Likely benign in CPLANE1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2026-01-29). AlphaMissense: likely benign (0.0954); Rare (popmax 0.351%, sas).

How common is CPLANE1 p.Ser3082Thr (c.9244T>A) in the general population?

CPLANE1 p.Ser3082Thr (c.9244T>A) is rare (popmax 0.351%, sas) (gnomAD).

What do computational predictors say about CPLANE1 p.Ser3082Thr (c.9244T>A)?

AlphaMissense predicts likely benign (score 0.0954) — an in-silico prediction, not a clinical call.

CPLANE1 p.Ser3082Thr

c.9244T>A · rs545791930 · VCV1548594

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.0954 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.351%, sas)

Missense predictors

0/2 damaging

AlphaMissense, REVEL

Computational evidence

Protein change
AlphaMissense	0.0954	likely benign
REVEL	0.051	moderately benign-leaning
⇒ AlphaMissense and REVEL both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.053	GERP -2.5
Regional constraint	o/e 0.92	unconstrained · MANE · 139 kb · p 2.3e-06 · regional, not allelic
Overall
CADD	7.357	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM S3028T vs ClinVar S3082T) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.351% South Asian · 308/87,764 alleles

Filtering AF 0.319% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.306%

Overall 0.0203% 325/1,600,758 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.351%	285
Remaining individualsnot grpmax-eligible	0.0258%	3,878
Admixed American	0.00176%	56,826

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CPLANE1
Protein: p.Ser3082Thr
Coding: c.9244T>A
MANE Select: NM_001384732
dbSNP: rs545791930
Type: single nucleotide variant
Location: chr5:37120282 (GRCh38)
Gene constraint: LOEUF 0.728 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Residue 3082: a UniProt-annotated variant site (in ofd6; likely pathogenic)

Full CPLANE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CPLANE1 p.Ser3082= Likely benign ★ same residue
CPLANE1 c.1372-2A>G Pathogenic/Likely pathogenic ★★ same type
CPLANE1 c.2291+1G>A Likely pathogenic ★★ same type
CPLANE1 c.2291+2T>C Pathogenic/Likely pathogenic ★★ same type
CPLANE1 c.2292-1G>A Likely pathogenic ★★ same type
CPLANE1 c.2500+1G>A Likely pathogenic ★★ same type
CPLANE1 c.2920+1G>A Likely pathogenic ★★ same type
CPLANE1 c.3290-2A>G Pathogenic/Likely pathogenic ★★ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cplane1-p-ser3082thr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown