Is ABCC11 p.Pro78Ser (c.232C>T) pathogenic?

ABCC11 p.Pro78Ser (c.232C>T) is classified Benign in ABCC11 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2018-04-04). AlphaMissense: likely benign (0.1665); Low-frequency (popmax 2.24%, afr).

How common is ABCC11 p.Pro78Ser (c.232C>T) in the general population?

ABCC11 p.Pro78Ser (c.232C>T) is low-frequency (popmax 2.24%, afr) (gnomAD).

What do computational predictors say about ABCC11 p.Pro78Ser (c.232C>T)?

AlphaMissense predicts likely benign (score 0.1665) — an in-silico prediction, not a clinical call.

ABCC11 p.Pro78Ser

c.232C>T · rs112756835 · VCV710085

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1665 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 2.24%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1665	likely benign
REVEL	0.217	benign-leaning
SaProt	LLR -5.03	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 1.1	GERP -0.81, phastCons 0.65
Regional constraint	o/e 0.98	unconstrained · MANE · 65 kb · p 0.31 · regional, not allelic
Overall
CADD	9.508	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 2.24% African / African-American · 1,674/74,694 alleles

Filtering AF 2.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.12%

Overall 0.121% 1,937/1,605,710 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	2.24%	45
Admixed American	0.195%	513
Remaining individualsnot grpmax-eligible	0.195%	513
Middle Eastern	0.134%	745
Ashkenazi Jewishnot grpmax-eligible	0.0103%	9,745
South Asian	0.00334%	29,927
European (non-Finnish)	0.00119%	84,022

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: ABCC11
Protein: p.Pro78Ser
Coding: c.232C>T
MANE Select: NM_001370497
dbSNP: rs112756835
Type: single nucleotide variant
Location: chr16:48230441 (GRCh38)
Gene constraint: LOEUF 1.004 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.30

Full ABCC11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCC11 p.Pro78Leu Uncertain significance ★ ⚠ same residue
ABCC11 p.Ala414= Benign ★★ same type
ABCC11 p.Arg630Trp Likely benign ★★ ⚠ same type
ABCC11 p.Leu553= Benign ★★ same type
ABCC11 p.Met970Val Benign ★★ same type
ABCC11 p.Thr1328= Benign ★★ same type
ABCC11 p.Thr546Met Benign ★★ same type
ABCC11 p.Trp8Cys 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/abcc11-p-pro78ser (accessed [today's date]).

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