Is CD101 p.Gly789= (c.2367C>T) pathogenic?

CD101 p.Gly789= (c.2367C>T) is classified Likely benign in CD101 (ClinVar, No assertion criteria, 2 submitters; last evaluated 2023-02-28). Rare (popmax 0.247%, nfe); Associated with CD101-related disorder.

What condition is associated with CD101 p.Gly789= (c.2367C>T)?

CD101 p.Gly789= (c.2367C>T) is associated with CD101-related disorder (ClinVar).

How common is CD101 p.Gly789= (c.2367C>T) in the general population?

CD101 p.Gly789= (c.2367C>T) is rare (popmax 0.247%, nfe) (gnomAD).

CD101 p.Gly789=

c.2367C>T · rs147808609 · VCV3034619

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.247%, nfe)

Conditions

CD101-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.3	GERP -3.2
Overall
CADD	2.844	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.247% European (non-Finnish) · 2,914/1,179,924 alleles

Filtering AF 0.239% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.236%

Overall 0.199% 3,211/1,613,822 alleles · rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.411%	243
European (non-Finnish)grpmax	0.247%	405
African / African-American	0.0453%	2,207
Admixed American	0.00834%	11,988
Finnishnot grpmax-eligible	0.00156%	64,032

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: CD101
Protein: p.Gly789=
Coding: c.2367C>T
MANE Select: NM_001256106
dbSNP: rs147808609
Type: single nucleotide variant
Location: chr1:117021922 (GRCh38)
Gene constraint: LOEUF 0.889 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.76
Residue 789: the ig-like c2-type 6 domain

Full CD101 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CD101-related disorder

Similar variants

CD101 p.Gly789Asp Uncertain significance ★ ⚠ same residue
CD101 c.2004_2017+6del Uncertain significance same condition
CD101 p.Arg622His Benign ★★ same type
CD101 p.Arg933Gln Benign ★★ ⚠ same type
CD101 p.Asn225Ser Benign ★★ same type
CD101 p.Leu362Pro Benign ★★ same type
CD101 p.Ser525Arg Benign ★★ ⚠ same type
CD101 p.Ser985= Benign ★★ 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/cd101-p-gly789 (accessed [today's date]).

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