Is CD274 p.Pro146Thr (c.436C>A) pathogenic?

CD274 p.Pro146Thr (c.436C>A) is classified Uncertain significance in CD274 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-14). AlphaMissense: likely benign (0.0993); Very rare (popmax 0.00329%, sas).

How common is CD274 p.Pro146Thr (c.436C>A) in the general population?

CD274 p.Pro146Thr (c.436C>A) is very rare (popmax 0.00329%, sas) (gnomAD).

What do computational predictors say about CD274 p.Pro146Thr (c.436C>A)?

AlphaMissense predicts likely benign (score 0.0993) — an in-silico prediction, not a clinical call.

CD274 p.Pro146Thr

c.436C>A · VCV3264788

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0993 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00329%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0993	likely benign
REVEL	0.101	moderately benign-leaning
SaProt	LLR -7.68	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.9	GERP 1, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 12 kb · p 0.73 · regional, not allelic
Overall
CADD	14.73	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — 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 0.00329% South Asian · 3/91,082 alleles

Filtering AF 0.000875% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000443%

Overall 0.00031% 5/1,613,876 alleles · very rare exomes 5/1,461,560 · genomes 0/152,316 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00329%	30,361
European (non-Finnish)	0.00017%	589,911

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: CD274
Protein: p.Pro146Thr
Coding: c.436C>A
MANE Select: NM_014143
Type: single nucleotide variant
Location: chr9:5462875 (GRCh38)
Gene constraint: LOEUF 0.476 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 88.13 · 78 PDB
Residue 146: a turn; the ig-like c2-type domain

Full CD274 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CD274 p.Pro146Arg Likely benign ★ same residue
CD274 c.*2635A>G Benign ★★ same type
CD274 c.*93G>A Benign ★★ same type
CD274 p.Arg186Ser Uncertain significance ★ ⚠ same type
CD274 p.Asn183Thr Uncertain significance ★ ⚠ same type
CD274 p.Asn278His Uncertain significance ★ ⚠ same type
CD274 p.Glu205Asp Uncertain significance ★ ⚠ same type
CD274 p.Glu217Lys 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/cd274-p-pro146thr (accessed [today's date]).

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