Is CD9 p.Glu103Gln (c.307G>C) pathogenic?

CD9 p.Glu103Gln (c.307G>C) is classified Uncertain significance in CD9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-12). AlphaMissense: likely pathogenic (0.7974); Very rare (popmax 0.00297%, nfe).

How common is CD9 p.Glu103Gln (c.307G>C) in the general population?

CD9 p.Glu103Gln (c.307G>C) is very rare (popmax 0.00297%, nfe) (gnomAD).

What do computational predictors say about CD9 p.Glu103Gln (c.307G>C)?

AlphaMissense predicts likely pathogenic (score 0.7974) — an in-silico prediction, not a clinical call.

CD9 p.Glu103Gln

c.307G>C · rs761288196 · VCV2518269

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7974 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00297%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.7974	likely pathogenic
REVEL	0.567	indeterminate
SaProt	LLR -7.67	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.2, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 37 kb · p 0.018 · regional, not allelic
Overall
CADD	28.2	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

Grpmax group 0.00297% European (non-Finnish) · 35/1,179,998 alleles

Filtering AF 0.00215% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00191%

Overall 0.00242% 39/1,614,018 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0064%	15,623
European (non-Finnish)grpmax	0.00297%	33,714

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: CD9
Protein: p.Glu103Gln
Coding: c.307G>C
MANE Select: NM_001769
dbSNP: rs761288196
Type: single nucleotide variant
Location: chr12:6233445 (GRCh38)
Gene constraint: LOEUF 0.555 · pLI 0.93 (gnomAD)
Structure: AlphaFold pLDDT 88.38 · 5 PDB
Residue 103: an α-helix

Full CD9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD9 c.447+8G>A Benign ★★ same type
CD9 p.Asn51Thr Uncertain significance ★ ⚠ same type
CD9 p.Gly210Ala Uncertain significance ★ ⚠ same type
CD9 p.Gly80Arg Uncertain significance ★ ⚠ same type
CD9 p.Leu96Phe Uncertain significance ★ ⚠ same type
CD9 p.Lys186Glu Uncertain significance ★ ⚠ same type
CD9 p.Met227Leu Uncertain significance ★ ⚠ same type
CD9 p.Met70Ile 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/cd9-p-glu103gln (accessed [today's date]).

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