Is CFAP36 p.Val12Leu (c.34G>T) pathogenic?

CFAP36 p.Val12Leu (c.34G>T) is classified Uncertain significance in CFAP36 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-22). AlphaMissense: likely pathogenic (0.8239); Absent from gnomAD v4.1.

How common is CFAP36 p.Val12Leu (c.34G>T) in the general population?

CFAP36 p.Val12Leu (c.34G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CFAP36 p.Val12Leu (c.34G>T)?

AlphaMissense predicts likely pathogenic (score 0.8239) — an in-silico prediction, not a clinical call.

CFAP36 p.Val12Leu

c.34G>T · VCV3832281

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8239 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8239	likely pathogenic
REVEL	0.199	benign-leaning
SaProt	LLR -8.99	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6.5	GERP -0.44, phastCons 1
Regional constraint	o/e 1.03	unconstrained · MANE · 25 kb · p 0.59 · regional, not allelic
Overall
CADD	23.7	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CFAP36
Protein: p.Val12Leu
Coding: c.34G>T
MANE Select: NM_080667
Type: single nucleotide variant
Location: chr2:55519835 (GRCh38)
Gene constraint: LOEUF 0.867 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.92

Full CFAP36 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP36 p.Ala332Thr Uncertain significance ★ ⚠ same type
CFAP36 p.Arg126Gln Uncertain significance ★ ⚠ same type
CFAP36 p.Arg176Thr Uncertain significance ★ ⚠ same type
CFAP36 p.Arg21Pro Uncertain significance ★ ⚠ same type
CFAP36 p.Arg280Thr Uncertain significance ★ ⚠ same type
CFAP36 p.Arg328Lys Uncertain significance ★ ⚠ same type
CFAP36 p.Asn132Ser Uncertain significance ★ ⚠ same type
CFAP36 p.Asp144Asn Uncertain significance ★ ⚠ 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/cfap36-p-val12leu (accessed [today's date]).

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