Is SRC p.Pro532= (c.1596C>G) pathogenic?

SRC p.Pro532= (c.1596C>G) is classified Likely benign in SRC (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-12-03). Rare (popmax 0.166%, mid); Associated with SRC-related disorder.

What condition is associated with SRC p.Pro532= (c.1596C>G)?

SRC p.Pro532= (c.1596C>G) is associated with SRC-related disorder (ClinVar).

How common is SRC p.Pro532= (c.1596C>G) in the general population?

SRC p.Pro532= (c.1596C>G) is rare (popmax 0.166%, mid) (gnomAD).

SRC p.Pro532=

c.1596C>G · rs751359112 · VCV3047023

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.166%, mid)

Conditions

SRC-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 -11	GERP -4.2
Overall
CADD	0.582	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.166% Middle Eastern · 10/6,036 alleles

Filtering AF 0.0898% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0684%

Overall 0.000689% 10/1,451,128 alleles · rare

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: SRC
Protein: p.Pro532=
Coding: c.1596C>G
MANE Select: NM_198291
dbSNP: rs751359112
Type: single nucleotide variant
Location: chr20:37403364 (GRCh38)
Gene constraint: LOEUF 0.383 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.59 · 79 PDB

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

Disease context

SRC-related disorder

Similar variants

SRC p.Glu527Lys Pathogenic/Likely pathogenic ★★ same condition
SRC c.450-8A>T Likely benign same condition
SRC p.Glu283= Likely benign same condition
SRC p.Phe175= Likely benign same condition
SRC p.Ser212= Likely benign same condition
SRC p.Glu492Lys Uncertain significance ★★ ⚠ same type
SRC c.1117-180C>T Benign ★★ same type
SRC c.1117-9C>T Likely 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/src-p-pro532 (accessed [today's date]).

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