Is CATIP p.Gly102Arg (c.304G>A) pathogenic?

CATIP p.Gly102Arg (c.304G>A) is classified Uncertain significance in CATIP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-02). AlphaMissense: ambiguous (0.3977); Ultra-rare (popmax 0.0725%, sas).

How common is CATIP p.Gly102Arg (c.304G>A) in the general population?

CATIP p.Gly102Arg (c.304G>A) is ultra-rare (popmax 0.0725%, sas) (gnomAD).

What do computational predictors say about CATIP p.Gly102Arg (c.304G>A)?

AlphaMissense predicts ambiguous (score 0.3977) — an in-silico prediction, not a clinical call.

CATIP p.Gly102Arg

c.304G>A · VCV4648581

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.3977 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0725%, sas)

Computational evidence

Protein change
AlphaMissense	0.3977	ambiguous
REVEL	0.384	indeterminate
SaProt	LLR -7.17	tolerated
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.25 · evaluated, not missing
Constraint at this position
Conservation	phyloP 6.3	GERP 0.86, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 11 kb · p 0.75 · regional, not allelic
Overall
CADD	26.8	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 0.0725% South Asian · 66/91,082 alleles

Filtering AF 0.0584% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0533%

Overall 0.00601% 97/1,613,350 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0725%	1,380
Middle Eastern	0.0167%	5,974
Finnishnot grpmax-eligible	0.011%	9,082
African / African-American	0.0107%	9,359
Remaining individualsnot grpmax-eligible	0.0064%	15,620
European (non-Finnish)	0.000932%	107,272

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: CATIP
Protein: p.Gly102Arg
Coding: c.304G>A
MANE Select: NM_198559
Type: single nucleotide variant
Location: chr2:218357719 (GRCh38)
Gene constraint: LOEUF 1.144 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.37

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

Similar variants

CATIP p.Ala363Thr Uncertain significance ★★ ⚠ same type
CATIP p.Ser57Leu Uncertain significance ★★ ⚠ same type
CATIP p.Phe35Ile Likely pathogenic ★ ⚠ same type
CATIP p.Ala348Thr Uncertain significance ★ ⚠ same type
CATIP p.Arg187Gln Uncertain significance ★ ⚠ same type
CATIP p.Arg195Cys Uncertain significance ★ ⚠ same type
CATIP p.Arg311Gln Uncertain significance ★ ⚠ same type
CATIP p.Arg383Gly 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/catip-p-gly102arg (accessed [today's date]).

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