Is SRC p.Asn196= (c.588C>T) pathogenic?

SRC p.Asn196= (c.588C>T) is classified Likely benign in SRC (ClinVar, Single submitter, 2 submitters; last evaluated 2024-11-01). Rare (popmax 0.232%, sas).

How common is SRC p.Asn196= (c.588C>T) in the general population?

SRC p.Asn196= (c.588C>T) is rare (popmax 0.232%, sas) (gnomAD).

SRC p.Asn196=

c.588C>T · VCV3358112

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.232%, sas)

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	6.821	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.232% South Asian · 211/91,082 alleles

Filtering AF 0.206% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.196%

Overall 0.112% 1,810/1,613,904 alleles · rare exomes 1,705/1,461,534 · genomes 105/152,370 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.232%	432
European (non-Finnish)	0.126%	793
Remaining individualsnot grpmax-eligible	0.0784%	1,276
Admixed American	0.0383%	2,610
East Asian	0.0379%	2,640
African / African-American	0.0253%	3,951
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,600
Finnishnot grpmax-eligible	0.00314%	31,897

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.Asn196=
Coding: c.588C>T
MANE Select: NM_198291
Type: single nucleotide variant
Location: chr20:37396196 (GRCh38)
Gene constraint: LOEUF 0.383 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.59 · 79 PDB
Residue 196: the sh2 domain; a turn

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

Similar variants

SRC p.Glu527Lys Pathogenic/Likely pathogenic ★★ same type
SRC p.Glu492Lys Uncertain significance ★★ ⚠ same type
SRC c.1117-180C>T Benign ★★ same type
SRC c.1117-9C>T Likely benign ★★ same type
SRC c.1271-55= Benign ★★ same type
SRC c.449+9C>T Benign/Likely benign ★★ same type
SRC c.553+8C>T Benign/Likely benign ★★ same type
SRC c.554-5C>T 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-asn196 (accessed [today's date]).

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