Is CALHM1 p.Pro111Ser (c.331C>T) pathogenic?

CALHM1 p.Pro111Ser (c.331C>T) is classified Uncertain significance in CALHM1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-29). AlphaMissense: likely pathogenic (0.9584); Very rare (popmax 0.00221%, nfe).

How common is CALHM1 p.Pro111Ser (c.331C>T) in the general population?

CALHM1 p.Pro111Ser (c.331C>T) is very rare (popmax 0.00221%, nfe) (gnomAD).

What do computational predictors say about CALHM1 p.Pro111Ser (c.331C>T)?

AlphaMissense predicts likely pathogenic (score 0.9584) — an in-silico prediction, not a clinical call.

CALHM1 p.Pro111Ser

c.331C>T · VCV4218315

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9584 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00221%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9584	likely pathogenic
REVEL	0.764	pathogenic-leaning
SaProt	LLR -10.07	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.92	unconstrained · MANE · 3,486 bp · p 0.085 · regional, not allelic
Overall
CADD	25.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00221% European (non-Finnish) · 26/1,177,414 alleles

Filtering AF 0.00154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0013%

Overall 0.00199% 32/1,609,660 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.00803%	12,461
European (non-Finnish)grpmax	0.00221%	45,285
African / African-American	0.00134%	74,856

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: CALHM1
Protein: p.Pro111Ser
Coding: c.331C>T
MANE Select: NM_001001412
Type: single nucleotide variant
Location: chr10:103458421 (GRCh38)
Gene constraint: LOEUF 1.293 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.25 · 4 PDB
Residue 111: the 'phospholipid-binding' region; a disulfide bond; an α-helix

Full CALHM1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CALHM1 p.Ala153Thr Benign ★★ same type
CALHM1 p.Arg154His Likely pathogenic ★ ⚠ same type
CALHM1 p.Ala107Thr Uncertain significance ★ ⚠ same type
CALHM1 p.Ala110Val Uncertain significance ★ ⚠ same type
CALHM1 p.Ala137Thr Uncertain significance ★ ⚠ same type
CALHM1 p.Ala172Pro Uncertain significance ★ ⚠ same type
CALHM1 p.Ala186Val Uncertain significance ★ ⚠ same type
CALHM1 p.Ala212Ser 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/calhm1-p-pro111ser (accessed [today's date]).

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