Is PSPH p.Leu79Phe (c.235C>T) pathogenic?

PSPH p.Leu79Phe (c.235C>T) is classified Uncertain significance in PSPH (ClinVar, Single submitter, 1 submitter; last evaluated 2018-03-23). AlphaMissense: likely benign (0.2343); Rare (popmax 0.1%, eas); Associated with PSPH deficiency.

What condition is associated with PSPH p.Leu79Phe (c.235C>T)?

PSPH p.Leu79Phe (c.235C>T) is associated with PSPH deficiency (ClinVar).

How common is PSPH p.Leu79Phe (c.235C>T) in the general population?

PSPH p.Leu79Phe (c.235C>T) is rare (popmax 0.1%, eas) (gnomAD).

What do computational predictors say about PSPH p.Leu79Phe (c.235C>T)?

AlphaMissense predicts likely benign (score 0.2343) — an in-silico prediction, not a clinical call.

PSPH p.Leu79Phe

c.235C>T · rs201222280 · VCV910294

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2343 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.1%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

PSPH deficiency

Computational evidence

Protein change
AlphaMissense	0.2343	likely benign
REVEL	0.289	benign-leaning
SaProt	LLR -10.78	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.5	GERP 2.8, phastCons 1
Regional constraint	o/e 0.81	unconstrained · MANE · 9,447 bp · p 0.0022 · regional, not allelic
Overall
CADD	16.74	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 0.1% East Asian · 45/44,880 alleles

Filtering AF 0.077% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0688%

Overall 0.00291% 47/1,613,968 alleles · rare exomes 43/1,461,652 · genomes 4/152,316 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.1%	997
Remaining individualsnot grpmax-eligible	0.0016%	62,494
South Asian	0.0011%	91,074

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: PSPH
Protein: p.Leu79Phe
Coding: c.235C>T
MANE Select: NM_004577
dbSNP: rs201222280
Type: single nucleotide variant
Location: chr7:56019640 (GRCh38)
Gene constraint: LOEUF 1.063 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.88 · 6 PDB
Residue 79: an α-helix

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

Disease context

PSPH deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

PSPH p.Arg101Ter Likely pathogenic ★★ same condition
PSPH c.422-3A>C Uncertain significance ★★ same condition
PSPH c.570+3A>G Uncertain significance ★★ same condition
PSPH c.570+5G>C Uncertain significance ★★ same condition
PSPH c.*341G>A Uncertain significance ★★ same condition
PSPH p.Asn124Ser Uncertain significance ★★ ⚠ same condition
PSPH p.Asp32Asn Uncertain significance ★★ ⚠ same condition
PSPH p.Gln204His Uncertain significance ★★ ⚠ same condition

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/psph-p-leu79phe (accessed [today's date]).

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