Is CHMP1A p.Ser67= (c.201C>T) pathogenic?

CHMP1A p.Ser67= (c.201C>T) is classified Uncertain significance in CHMP1A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-27). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with CHMP1A p.Ser67= (c.201C>T)?

CHMP1A p.Ser67= (c.201C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CHMP1A p.Ser67= (c.201C>T) in the general population?

CHMP1A p.Ser67= (c.201C>T) is absent from gnomAD v4.1 (gnomAD).

CHMP1A p.Ser67=

c.201C>T · rs2543451939 · VCV3144422

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.147	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.73	GERP -3.4, phastCons 1
Overall
CADD	5.702	PHRED · no single calibrated threshold — expert panels disagree

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: CHMP1A
Protein: p.Ser67=
Coding: c.201C>T
MANE Select: NM_002768
dbSNP: rs2543451939
Type: single nucleotide variant
Location: chr16:89649402 (GRCh38)
Gene constraint: LOEUF 1.045 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.44 · 4 PDB

Full CHMP1A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHMP1A p.Ala172Thr Uncertain significance ★★ ⚠ same condition
CHMP1A p.Arg46Cys Uncertain significance ★★ ⚠ same condition
CHMP1A p.Arg54Cys Uncertain significance ★★ ⚠ same condition
CHMP1A p.Arg64Trp Uncertain significance ★★ ⚠ same condition
CHMP1A p.Gly59Ser Uncertain significance ★★ ⚠ same condition
CHMP1A p.Lys27Asn Uncertain significance ★★ same condition
CHMP1A p.Ser127Trp Uncertain significance ★★ ⚠ same condition
CHMP1A p.Ser135= Uncertain significance ★★ same condition

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/chmp1a-p-ser67 (accessed [today's date]).

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